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Rapport.html
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Rapport.html
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<!doctype html>
<html style='font-size:10px !important'>
<head>
<meta charset='UTF-8'><meta name='viewport' content='width=device-width initial-scale=1'>
<title>README</title><style type='text/css'>html {overflow-x: initial !important;}:root { --bg-color:#ffffff; --text-color:#333333; --select-text-bg-color:#B5D6FC; --select-text-font-color:auto; --monospace:"Lucida Console",Consolas,"Courier",monospace; }
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<div id='write' class = ' first-line-indent'><h1><a name="polledhic" class="md-header-anchor"></a><span>PolledHiC</span></h1><div class='md-toc' mdtype='toc'><p class="md-toc-content" role="list"><span role="listitem" class="md-toc-item md-toc-h1" data-ref="n3845"><a class="md-toc-inner" href="#polledhic">PolledHiC</a></span><span role="listitem" class="md-toc-item md-toc-h1" data-ref="n3849"><a class="md-toc-inner" href="#introduction">Introduction</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n3853"><a class="md-toc-inner" href="#la-méthode-hic-">La méthode HiC :</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n3871"><a class="md-toc-inner" href="#les-données-seqoccin-">Les données SeqOccin :</a></span><span role="listitem" class="md-toc-item md-toc-h1" data-ref="n3880"><a class="md-toc-inner" href="#nf-corehic">NF-Core/HiC</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n3883"><a class="md-toc-inner" href="#workflow">Workflow</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n3898"><a class="md-toc-inner" href="#multiqc">MultiQC</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n3916"><a class="md-toc-inner" href="#tableau-récapitulatif-des-données-">Tableau récapitulatif des données :</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4083"><a class="md-toc-inner" href="#les-matrices-de-contacts">Les matrices de contacts</a></span><span role="listitem" class="md-toc-item md-toc-h1" data-ref="n4089"><a class="md-toc-inner" href="#conda--polledhicenv">Conda : polledHiC_env</a></span><span role="listitem" class="md-toc-item md-toc-h1" data-ref="n4096"><a class="md-toc-inner" href="#hicexplorer">hicExplorer</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4099"><a class="md-toc-inner" href="#convertformat">ConvertFormat</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4104"><a class="md-toc-inner" href="#summatrices">SumMatrices</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4108"><a class="md-toc-inner" href="#adjustmatrix">AdjustMatrix</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4111"><a class="md-toc-inner" href="#normalize-et-correctmatrix">Normalize et CorrectMatrix</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4118"><a class="md-toc-inner" href="#diagnostic-plot">Diagnostic plot</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4129"><a class="md-toc-inner" href="#carte-hic">Carte HiC</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4144"><a class="md-toc-inner" href="#recherche-de-tads">Recherche de TADs</a></span><span role="listitem" class="md-toc-item md-toc-h3" data-ref="n4146"><a class="md-toc-inner" href="#hicfindtads-">hicFindTADs :</a></span><span role="listitem" class="md-toc-item md-toc-h3" data-ref="n4159"><a class="md-toc-inner" href="#hicplottads-">hicPlotTADs :</a></span><span role="listitem" class="md-toc-item md-toc-h1" data-ref="n4170"><a class="md-toc-inner" href="#snakemake-et-automatisation">Snakemake et automatisation</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4181"><a class="md-toc-inner" href="#nfcore-hic">nfcore-hic</a></span><span role="listitem" class="md-toc-item md-toc-h3" data-ref="n4183"><a class="md-toc-inner" href="#nfcore-hicconfig">nfcore-hic.config</a></span><span role="listitem" class="md-toc-item md-toc-h3" data-ref="n4185"><a class="md-toc-inner" href="#nfcore-hicsh">nfcore-hic.sh</a></span><span role="listitem" class="md-toc-item md-toc-h2" data-ref="n4201"><a class="md-toc-inner" href="#hicexplorer-n4201">hicexplorer</a></span><span role="listitem" class="md-toc-item md-toc-h3" data-ref="n4213"><a class="md-toc-inner" href="#configyaml">config.yaml</a></span><span role="listitem" class="md-toc-item md-toc-h3" data-ref="n4218"><a class="md-toc-inner" href="#makesampledprotocolpy">make_sampled_protocol.py</a></span><span role="listitem" class="md-toc-item md-toc-h3" data-ref="n4224"><a class="md-toc-inner" href="#snakefile">Snakefile</a></span><span role="listitem" class="md-toc-item md-toc-h3" data-ref="n4229"><a class="md-toc-inner" href="#hicexplorersh">hicexplorer.sh</a></span><span role="listitem" class="md-toc-item md-toc-h1" data-ref="n4237"><a class="md-toc-inner" href="#tldr--comment-lancer-une-analyse-sur-genologin-">TL;DR : Comment lancer une analyse sur Genologin :</a></span></p></div><p> </p><h1><a name="introduction" class="md-header-anchor"></a><span>Introduction</span></h1><p><span>Le projet PolledHiC est un projet réalisé dans le cadre d'un stage facultatif de Master 1 Bioinformatique et Biologie des systèmes.</span></p><p><span>Il a été initié par Thomas FARAUT et Alain PINTON (INRAE Occitanie - UMR GenPhySE). </span></p><p><span>Le projet consiste à traiter les données de séquençage HiC de l'équipe de SeqOccin pour tenter d'obtenir des cartes chromosomiques de différentes régions d’intérêts chez les bovins. Le but est de fournir un pipeline permettant l'analyse et la comparaison des structures tri-dimensionnelle entre les phénotypes 'avec cornes' et 'sans cornes' chez certains d'entre eux.</span></p><h2><a name="la-méthode-hic-" class="md-header-anchor"></a><span>La méthode HiC :</span></h2><p><span>La méthode de séquençage HiC ( High Chromosome Contact map ), est une technique de séquençage haut débits permettant d'étudier les interactions au niveau génétique.</span></p><p><span>Les étapes sont les suivantes :</span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/hic.jpg" referrerpolicy="no-referrer"></p><ul><li><span>Cross-link pour 'figer' les chromosomes.</span></li><li><span>Digestion par des enzymes de restrictions.</span></li><li><span>Ligation des fragments cross-linker.</span></li><li><span>Élimination du 'cross-link'</span></li><li><span>Filtrage des séquences sur les régions d'intérêt</span></li><li><span>Visualisation (cartes HiC et plot TADs)</span></li></ul><p> </p><h2><a name="les-données-seqoccin-" class="md-header-anchor"></a><span>Les données SeqOccin :</span></h2><p><span>Les données ont été obtenus par le biais du projet « </span><strong><span>Séquençage Occitanie Innovation</span></strong><span> » (soit SeqOccin). </span></p><p><span>Elles contiennent les informations de deux trio de bovins pour lesquels ont été réalisés :</span></p><ul><li><span>différents protocoles HiC (Arima, Dovetail, PhaseG et Maison).</span></li><li><span>différents runs avec différent niveaux de coverage.</span></li></ul><p><span>Dans le cadre de ce projet, les protocoles PhaseG n'ont pas été retenus.</span></p><h1><a name="nf-corehic" class="md-header-anchor"></a><span>NF-Core/HiC</span></h1><p><span>Le pipeline </span><strong><a href='https://github.com/nf-core/hic'><span>NF-Core/HiC</span></a></strong><span> est basé sur le workflow HiC-Pro. Il permet d'obtenir des matrices de contacts à partir de données brutes au format FastQ.</span></p><p><span>A l'issue de ces étapes, les manipulations sur les matrices de contacts seront réalisés via le logiciel </span><a href='https://github.com/deeptools/HiCExplorer'><span>HiCExplorer</span></a><span>.</span></p><h2><a name="workflow" class="md-header-anchor"></a><span>Workflow</span></h2><p><span>Le workflow de NF-Core/hic se réalise en X étapes :</span></p><ol start='' ><li><span>Alignements des reads</span></li><li><span>Appariements des reads</span></li><li><strong><span>Mapping</span></strong></li><li><span>Obtention de la matrice de contacts brut</span></li></ol><p><img src="/home/jeremy/Bureau/polledHiC/images/hicpro_wkflow.jpg" referrerpolicy="no-referrer"></p><p><span>Au cours de ce pipeline, l'étape de mapping va déterminer les "</span><strong><span>valid-pairs</span></strong><span>". C'est à partir de ces valid-pairs que la matrice de contact pourra être créer, l'étape de mapping est donc très importantes.</span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/hicpro_mapping_wkflow.jpg" referrerpolicy="no-referrer"></p><p><span>Tout ce qui n'est pas considéré comme une valid-pairs n'est pas retenu dans l'élaboration de la carte de contact. Ils peuvent être obtenue en première intention à l'issue des premières étapes d'alignements, où en seconde intention, après une étape de "trim" des fragments de restrictions / ligations.</span></p><h2><a name="multiqc" class="md-header-anchor"></a><span>MultiQC</span></h2><p><span>À l'issue de son processus, NF-Core/hic permet également d'obtenir un rapport </span><a href='https://multiqc.info/'><span>MultiQC</span></a><span>.</span></p><p><span>MultiQC est un outil permettant de présenter sous forme de rapport html les résultats de nombreux outils bio-informatiques. Ici ces rapports contiennent les résultats statistiques des étape de mapping et de construction de la carte de contact.</span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/multiqc.jpg" referrerpolicy="no-referrer"></p><p><strong><span>MAPPING STATISTICS :</span></strong></p><p><img src="/home/jeremy/Bureau/polledHiC/images/multiqc_mapping.jpg" referrerpolicy="no-referrer"></p><p><span>Il est attendu qu'une grosse majorité des reads soit directement aligné sur le génome (80 à 90%). Les 'trimmed reads alignments' correspondent aux reads alignées en seconde intention. Il s'agit de fragments chimériques qui sont détectés avec le fragments de ligation. Un niveau trop élevée de ces fragments chimériques peut être le reflet d'un problème lors de l'étape de ligation.</span></p><p><strong><span>PAIRING STATISTICS :</span></strong></p><p><img src="/home/jeremy/Bureau/polledHiC/images/multiqc_pairing.jpg" referrerpolicy="no-referrer"></p><p><span>Les reads sont censé être "paired". Le taux des fractions dépend grandement de la complexité du génome et de la fraction de reads non mappée. On s'attend à ce que la fraction de singleton soit proche de la fraction de reads non mappé. Un taux de singleton trop élevée et/ou différent du nombre de reads non mappé peut être révélateur d'un problème avec les données.</span></p><p><strong><span>FILTERING STATISCTICS :</span></strong></p><p><img src="/home/jeremy/Bureau/polledHiC/images/multiqc_filtering.jpg" referrerpolicy="no-referrer"></p><p><span>La qualité de l'analyse peut être évaluée en filtrant les paires de reads.</span></p><p><span>Comme la ligation est un processus aléatoire, on attend une répartition de 25% pour chaque classe de "</span><strong><span>valid-pairs</span></strong><span>" (</span><em><span>Forward-Forward</span></em><span>, </span><em><span>Forward-Reverse</span></em><span>, </span><em><span>Reverse-Forward</span></em><span> et </span><em><span>Reverse-Reverse</span></em><span>). De la même façon, une fraction élevée de </span><em><span>dangling-end</span></em><span> ou de </span><em><span>self-circle read pairs</span></em><span> est représentatif d'une faible qualité expérimentale et peut révéler un problème lors des étapes de digestion, d'élongation ou de ligation.</span></p><p><strong><span>CONTACT STATISTICS :</span></strong></p><p><img src="/home/jeremy/Bureau/polledHiC/images/multiqc_contact.jpg" referrerpolicy="no-referrer"></p><p><span>Il est généralement attendu d'observer une distribution centrée autour de la taille de l'insert utilisé. Il est normal d'observer une majorité de contact type cis- éloigné (plus de 20kb de distance sur un même chromosome) ou trans- (deux régions sur deux chromosomes différents).</span></p><p><span>La fraction des doublons est également présentée. Un niveau élevé de duplication indique une faible complexité moléculaire et un biais de PCR potentiel.</span></p><h2><a name="tableau-récapitulatif-des-données-" class="md-header-anchor"></a><span>Tableau récapitulatif des données :</span></h2><p><span>Voici ci dessous, un tableau récapitulatif des données utilisées :</span></p><figure><table><thead><tr><th><span>trio</span></th><th><span>animal</span></th><th><span>run</span></th><th><span>protocol</span></th><th><span>paired reads</span></th><th><span>valid pairs</span></th></tr></thead><tbody><tr><td><span>trio1</span></td><td><span>father</span></td><td><span>run1</span></td><td><span>Arima</span></td><td><span>89637817</span></td><td><span>22279893</span></td></tr><tr><td><span>trio1</span></td><td><span>father</span></td><td><span>run1</span></td><td><span>Dovetail</span></td><td><span>3700008</span></td><td><span>1866639</span></td></tr><tr><td><span>trio1</span></td><td><span>father</span></td><td><span>run1</span></td><td><span>Maison</span></td><td><span>141875156</span></td><td><span>66790091</span></td></tr><tr><td><span>trio1</span></td><td><span>father</span></td><td><span>run2</span></td><td><span>Arima</span></td><td><span>119832383</span></td><td><span>30993207</span></td></tr><tr><td><span>trio1</span></td><td><span>mother</span></td><td><span>run1</span></td><td><span>Arima</span></td><td><span>76366518</span></td><td><span>16817078</span></td></tr><tr><td><span>trio1</span></td><td><span>mother</span></td><td><span>run1</span></td><td><span>Dovetail</span></td><td><span>108323412</span></td><td><span>49112300</span></td></tr><tr><td><span>trio1</span></td><td><span>mother</span></td><td><span>run1</span></td><td><span>Maison</span></td><td><span>134238122</span></td><td><span>82351532</span></td></tr><tr><td><span>trio1</span></td><td><span>mother</span></td><td><span>run2</span></td><td><span>Arima</span></td><td><span>105484493</span></td><td><span>0</span></td></tr><tr><td><span>trio1</span></td><td><span>offspring</span></td><td><span>run1</span></td><td><span>Arima</span></td><td><span>1688139</span></td><td><span>387688</span></td></tr><tr><td><span>trio1</span></td><td><span>offspring</span></td><td><span>run1</span></td><td><span>Dovetail</span></td><td><span>1496149</span></td><td><span>437911</span></td></tr><tr><td><span>trio1</span></td><td><span>offspring</span></td><td><span>run1</span></td><td><span>Maison-minus</span></td><td><span>1541573</span></td><td><span>613689</span></td></tr><tr><td><span>trio1</span></td><td><span>offspring</span></td><td><span>run1</span></td><td><span>Maison-plus</span></td><td><span>1715720</span></td><td><span>976474</span></td></tr><tr><td><span>trio1</span></td><td><span>offspring</span></td><td><span>run2</span></td><td><span>Arima</span></td><td><span>130341495</span></td><td><span>30135249</span></td></tr><tr><td><span>trio1</span></td><td><span>offspring</span></td><td><span>run2</span></td><td><span>Dovetail</span></td><td><span>164244926</span></td><td><span>49182828</span></td></tr><tr><td><span>trio1</span></td><td><span>offspring</span></td><td><span>run2</span></td><td><span>Maison-plus</span></td><td><span>67743665</span></td><td><span>35536687</span></td></tr><tr><td><span>trio1</span></td><td><span>offspring</span></td><td><span>run3</span></td><td><span>Maison-plus</span></td><td><span>188344770</span></td><td><span>110398242</span></td></tr><tr><td><span>trio2</span></td><td><span>father</span></td><td><span>run1</span></td><td><span>Maison</span></td><td><span>128040893</span></td><td><span>11267457</span></td></tr><tr><td><span>trio2</span></td><td><span>father</span></td><td><span>run2</span></td><td><span>Maison</span></td><td><span>100015296</span></td><td><span>8456432</span></td></tr><tr><td><span>trio2</span></td><td><span>mother</span></td><td><span>run1</span></td><td><span>Maison</span></td><td><span>159863877</span></td><td><span>80781661</span></td></tr><tr><td><span>trio2</span></td><td><span>mother</span></td><td><span>run2</span></td><td><span>Maison</span></td><td><span>113850699</span></td><td><span>54282196</span></td></tr><tr><td><span>trio2</span></td><td><span>offspring</span></td><td><span>run1</span></td><td><span>Maison</span></td><td><span>141212982</span></td><td><span>75281563</span></td></tr><tr><td><span>trio2</span></td><td><span>offspring</span></td><td><span>run2</span></td><td><span>Maison</span></td><td><span>107893352</span></td><td><span>54602426</span></td></tr></tbody></table></figure><p><span>Au vu des informations précédentes, il a été établi que les paired reads et les valid-pairs sont déterminant dans la qualité de l'analyse qui en découle. </span></p><p><span>Il est observable que le trio1 mother run2 Arima n'a aucun valid-pairs. Il a été décidé que les deux runs ne seraient pas pris en compte. Il y avait donc 20 runs qui composait le matériel d'étude.</span></p><p><span>Il est également observable que les individus du trio2 présentent moins de données que le trio1. Cela se ressentira lors de l'analyse.</span></p><h2><a name="les-matrices-de-contacts" class="md-header-anchor"></a><span>Les matrices de contacts</span></h2><p><span>Les matrices de contacts se présentent sous la forme :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>4</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">A B 10</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">A C 23</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">B C 24</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">(...)</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 60px;"></div><div class="CodeMirror-gutters" style="height: 60px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>Ce format permet d'optimiser l'espace mémoire en ne tenant pas compte des interactions nulle (aucune valeur à 0). Il est également compatible avec d'autre logiciel d'analyse tel que HiTC Bioconductor package ou HiCPlotter software.</span></p><p><span>Cependant, ce format n'est pas directement pris en charge par hicExplorer, mais il est possible de le convertir au format hdf5 reconnu par l'outil.</span></p><p><span>A ce stade, il y a une matrice de contact par run et par résolutions étudiées (200000, 50000, 25000 et 10000 bins). Dans le cadre de l'étude, il y a donc 80 matrices de contacts.</span></p><h1><a name="conda--polledhicenv" class="md-header-anchor"></a><span>Conda : polledHiC_env</span></h1><p><span>Pour réaliser le reste des analyses, il est nécessaire d'utiliser la dernière version d'hicExplorer.</span></p><p><span>Pour s'assurer de la répétabilitée de la manipulation, il est conseillé de travailler sous un environnement conda identique à celui de l'étude :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>4</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">conda env create <span class="cm-attribute">-n</span> polledHiC_env <span class="cm-def">python</span><span class="cm-operator">=</span><span class="cm-number">3</span>.7.8</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">conda activate polledHiC_env</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">conda install <span class="cm-def">hicexplorer</span><span class="cm-operator">=</span><span class="cm-number">3</span>.5.1 <span class="cm-def">snakemake</span><span class="cm-operator">=</span><span class="cm-number">5</span>.14.0</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 60px;"></div><div class="CodeMirror-gutters" style="height: 60px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>Une autre façon est de télécharger </span><a href='https://github.com/StructVarGA/polledHiC/blob/master/workflows/polledHiC_env.txt'><span>ce fichier</span></a><span> </span><code>polledHiC_env.txt</code><span>, puis :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>3</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">conda create <span class="cm-attribute">--name</span> polledHiC_env <span class="cm-attribute">--file</span> polledHiC_env.txt</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">conda activate polledHiC_env</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 45px;"></div><div class="CodeMirror-gutters" style="height: 45px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>Dans les deux cas, il est indispensable d'activer l'environnement de travail pour que les étapes suivantes soient correctement exécuter.</span></p><h1><a name="hicexplorer" class="md-header-anchor"></a><span>hicExplorer</span></h1><p><span>hicExplorer est une suite d'outils permettant l'analyse de données HiC.</span></p><p><span>Le pipeline d'analyse réalisé utilise de nombreux outils et permet d'obtenir, à l'issue de ce dernier, une carte chromosomique à différente échelle centrée sur les 3 premiers millions de bases du chromosome 1.</span></p><h2><a name="convertformat" class="md-header-anchor"></a><span>ConvertFormat</span></h2><p><span>La première étape consiste à convertir les matrices hicpro vers un format hdf5 exploitable par le reste des outils d'hicExplorer :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>1</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">hicConvertFormat <span class="cm-attribute">--matrices</span> {input.raw} <span class="cm-attribute">--bedFileHicpro</span> {input.bed} <span class="cm-attribute">--outFileName</span> {output} <span class="cm-attribute">--inputFormat</span> hicpro <span class="cm-attribute">--outputFormat</span> h5</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 30px;"></div><div class="CodeMirror-gutters" style="height: 30px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>Le format HDF5 est un conteneur de fichier construit en ensemble de données. Cela donne aux fichiers HDF5 une structure en arborescence :</span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/hdf5.png" referrerpolicy="no-referrer"></p><h2><a name="summatrices" class="md-header-anchor"></a><span>SumMatrices</span></h2><p><span>La seconde étape consiste à sommer les matrices de même résolutions pour obtenir un maximum d'informations pour chaque individus.</span></p><p><span>Cela se fait en deux temps :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>5</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Merge runs by protocols</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">hicSumMatrices <span class="cm-attribute">--matrices</span> {input.indiv.protocol.h5} <span class="cm-attribute">--outFileName</span> {output.indiv.merged.protocol.h5}</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Merge protocols by indiv</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">hicSumMatrices <span class="cm-attribute">--matrices</span> {input.indiv.merged.protocol.h5} <span class="cm-attribute">--outFileName</span> {output.indiv.merged.h5}</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 105px;"></div><div class="CodeMirror-gutters" style="height: 105px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><h2><a name="adjustmatrix" class="md-header-anchor"></a><span>AdjustMatrix</span></h2><p><span>La commande hicAdjustMatrix permet de s'affranchir des contigs dans les données à analyser, et de ce concentrer uniquement sur les chromosomes complets.</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>1</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">hicAdjustMatrix <span class="cm-attribute">--matrix</span> {input.indiv.merged.h5} <span class="cm-attribute">--outFileName</span> {output.indiv.adjusted.h5} <span class="cm-attribute">--chromosomes</span> <span class="cm-number">1</span> <span class="cm-number">2</span> <span class="cm-number">3</span> <span class="cm-number">4</span> <span class="cm-number">5</span> <span class="cm-number">6</span> <span class="cm-number">7</span> <span class="cm-number">8</span> <span class="cm-number">9</span> <span class="cm-number">10</span> <span class="cm-number">11</span> <span class="cm-number">12</span> <span class="cm-number">13</span> <span class="cm-number">14</span> <span class="cm-number">15</span> <span class="cm-number">16</span> <span class="cm-number">17</span> <span class="cm-number">18</span> <span class="cm-number">19</span> <span class="cm-number">20</span> <span class="cm-number">21</span> <span class="cm-number">22</span> <span class="cm-number">23</span> <span class="cm-number">24</span> <span class="cm-number">25</span> <span class="cm-number">26</span> <span class="cm-number">27</span> <span class="cm-number">28</span> <span class="cm-number">29</span> X <span class="cm-attribute">--action</span> keep</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 45px;"></div><div class="CodeMirror-gutters" style="height: 45px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><h2><a name="normalize-et-correctmatrix" class="md-header-anchor"></a><span>Normalize et CorrectMatrix</span></h2><p><span>Les développeurs d'hicExplorer recommandent de réaliser une normalisation avant la correction de la matrice </span><em><span>(cf. la documentation de </span><a href='https://hicexplorer.readthedocs.io/en/latest/content/tools/hicNormalize.html#hicnormalize'><span>hicNormalize sur </span><strong><span>readthedocs.io</span></strong></a><span>)</span></em><span>.</span></p><p><span>La normalisation des matrices de données permet de normaliser au plus petit nombre de lecture donné de toutes les matrices ou à une plage de 0 à 1.</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>1</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">hicNormalize <span class="cm-attribute">--matrices</span> {input.indiv.adjusted.h5} <span class="cm-attribute">--outFileName</span> {output.indiv.normalized.h5} <span class="cm-attribute">--normalize</span> smallest</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 30px;"></div><div class="CodeMirror-gutters" style="height: 30px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>La correction quant à elle permet d'éliminer les biais induit par les régions riches en GC, et normaliser le nombre de sites de restriction par bins. Étant donné qu'une fraction des bins peuvent être issue de régions fortement répétées, ces bins contiennent peu de contact et il est nécessaire de les filtrer.</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>1</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">hicCorrectMatrix correct <span class="cm-attribute">--matrix</span> {input.indiv.normalized.h5} <span class="cm-attribute">--outFileName</span> {output.indiv.corrected.h5}</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 30px;"></div><div class="CodeMirror-gutters" style="height: 30px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>A l'issue de cette étape, il a été obtenu pour chaque individus, quatre matrices finales (une pour chaque résolutions) prêtes à être analyser. </span></p><h2><a name="diagnostic-plot" class="md-header-anchor"></a><span>Diagnostic plot</span></h2><p><span>Le diagnostic plot est un histogramme de la fréquence de comptage par bins. Cet histogramme permet de comparer les différentes résolutions sur un même jeu de données. Il est attendu d'observer une répartition Normale.</span></p><p><span>Le modified Z-Score est un indicateur permettant d'identifier les outliers de nos données. Le trait bleu sur ces histogrammes marque le MAD Z-Score : Median Absolute Deviation. C'est la valeur par défaut prise lors de la correction pour éliminer ces outliers.</span></p><p><span>Le choix de la bonne résolution est cruciale dans la qualité d'analyse, et dépend des données analysées :</span></p><p><span>Avec une résolution à 200.000 pb par bins, on observe chez Trio1 Father une répartition qui est loin de s'apparenter à une Gaussienne.</span>
<img src="/home/jeremy/Bureau/polledHiC/images/diagnostics/trio1.father_merged_200000_diagnostic.png" referrerpolicy="no-referrer" alt="Trio1 Father merged at 200k bins"></p><p><span>De la même manière, avec une résolution trop fine, certains jeu de données peuvent donner des résultats incompatibles avec la suite des analyses. Ici on observe l'individu Trio2 Offspring à une résolution de 10.000 pb par bins : </span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/diagnostics/trio2.offspring_merged_10000_diagnostic.png" referrerpolicy="no-referrer" alt="Trio2 Offspring merged at 10k bins"></p><p><span>En choisissant une résolution adéquate avec les données, on retrouve alors une répartition s'apparentant à une Normale, comme par exemple ici, avec Trio1 Offspring à 25k bins :</span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/diagnostics/trio1.offspring_merged_25000_diagnostic.png" referrerpolicy="no-referrer"></p><p><span>On observe un gros pics à 0. Les étapes d'ajustement et de correction permettent d'éliminer ces biais. Voici le diagnostic plot du même individu, à la même résolution, après réalisation de ces étapes :</span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/diagnostics/25k_normalized.png" referrerpolicy="no-referrer"></p><h2><a name="carte-hic" class="md-header-anchor"></a><span>Carte HiC</span></h2><p><span>Enfin, il devient alors possible de créer les cartes de contacts des régions qui nous intéressent à partir des résultats précédents. </span></p><p><span>Dans le but d'établir un profil, il a été créé un individus </span><strong><span>"Consensus"</span></strong><span> issue de la somme des matrices finales de chaque individus. </span></p><p><span>La résolutions d'études va également dépendre de la fenêtre qui va nous intéresser. Plus cette fenêtre est grande, moins on doit être résolutif :</span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/cons_10_vs_200k.png" referrerpolicy="no-referrer"></p><p><span>La fenêtre choisis va des positions 1M à 3M de bases sur le chromosome 1. Nous nous concentrerons donc sur les plus fortes résolutions : 10.000 pb et 25.000 pb par bins.</span></p><p><span>Cette fenêtre a été choisi pour prendre en compte les mutations Celtic, Friesian, Mongolian et Guarani situé entre les positions 2M4 et 2M7.</span></p><p><strong><span>10k bins resolutions :</span></strong></p><p><img src="/home/jeremy/Bureau/polledHiC/images/plots_10k.png" referrerpolicy="no-referrer"></p><p><strong><span>25k bins resolutions :</span></strong></p><p><img src="/home/jeremy/Bureau/polledHiC/images/plots_25k.png" referrerpolicy="no-referrer"></p><p><span>Au vu des données possédés, il semblerait que la résolution 25k bins soit la plus adéquate pour analyser nos données. On notera toute fois que la mise en place de l'individu "</span><em><span>Consensus</span></em><span>" a permis d'obtenir des résultats plus probant à la résolution 10k bins que les individus.</span></p><p><span>On observe alors la formation de </span><strong><span>TADs</span></strong><span> </span><em><span>(</span><strong><span>T</span></strong><span>opologically </span><strong><span>A</span></strong><span>ssociated </span><strong><span>D</span></strong><span>omains)</span></em><span> sur ces cartes. Ces TADs sont représentés par des </span><em><span>"carrés"</span></em><span> sur la diagonale de la carte, notamment entre les positions 1.20 et 1.65 , 1.70 et 1.95 , 2.00 et 2.40 et enfin entre 2.40 et 2.75.</span></p><p><span>Il semblerait également que la matrices consensus permette de retrouver ces patterns à la résolution 10k bins contrairement aux matrices issue des individus.</span></p><p><span>Cet interprétation n'étant qu'une interprétation graphique, il s'en suit donc une dernière étape : la recherche et la caractérisation des TADs.</span></p><h2><a name="recherche-de-tads" class="md-header-anchor"></a><span>Recherche de TADs</span></h2><p><span>La recherche de TADs se fait via les outils </span><code>hicFindTADs</code><span> et </span><code>hicPlotTADs</code></p><h3><a name="hicfindtads-" class="md-header-anchor"></a><span>hicFindTADs :</span></h3><p><span>La fonction hicFindTADs mesure le TAD-separation score pour identifier des degrés de séparation sur chaque bins de la matrice hic.</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>2</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">hicFindTADs <span class="cm-attribute">--matrix</span> {input} <span class="cm-attribute">--outPrefix</span> {outprefix} \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-attribute">--correctForMultipleTesting</span> fdr <span class="cm-attribute">--chromosomes</span> <span class="cm-number">1</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 30px;"></div><div class="CodeMirror-gutters" style="height: 30px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>En sortie de cette fonction, il y a plusieurs fichiers produits : </span></p><ul><li><strong><span>{outprefix}</span><span>_</span><span>boundaries.bed et {outprefix}</span><span>_</span><span>boundaries.gff</span></strong><span> : contiennent les informations sur les frontières de TADs.</span></li><li><strong><span>{outprefix}</span><span>_</span><span>domains.bed</span></strong><span> : contient les positions des TADs.</span></li><li><strong><span>{outprefix}</span><span>_</span><span>score.bedgraph et {outprefix}</span><span>_</span><span>score.bm</span></strong><span> : contiennent les TAD-separation score. Le fichier score.bm est une 'matrice bedgraph' qui peut être utiliser pour la représentation graphique des TAD-separation score dans hicPlotTADs.</span></li><li><strong><span>{outprefix}</span><span>_</span><span>zscore_matrix.h5</span></strong><span> : contient les matrices où les score ont été remplacés par les z-score (nécessaire pour la création des fichiers boundaries).</span></li></ul><h3><a name="hicplottads-" class="md-header-anchor"></a><span>hicPlotTADs :</span></h3><p><span>En plus des sortie de </span><code>hicFindTADs</code><span>, il est nécessaire de mettre en place un fichier </span><code>tracks.ini</code><span> pour plotter correctement les TADs.</span></p><p><span>Ces fichiers sont composé comme ci-dessous :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash" style="break-inside: unset;"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 50.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 37px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>33</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -37px; width: 37px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[x-axis]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-def">fontsize</span><span class="cm-operator">=</span><span class="cm-number">10</span> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[hic matrix] </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file <span class="cm-operator">=</span> <span class="cm-comment"># path/to/matrix/corrected.h5</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">title <span class="cm-operator">=</span> <span class="cm-comment"># title i.e. 'sample_resolution'</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># depth is the maximum distance plotted in bp. In Hi-C tracks </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># the height of the track is calculated based on the depth such </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># that the matrix does not look deformed </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">10</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">colormap <span class="cm-operator">=</span> Spectral_r </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">11</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">depth <span class="cm-operator">=</span> <span class="cm-number">1500000</span> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">12</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">transform <span class="cm-operator">=</span> log1p </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">13</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file_type <span class="cm-operator">=</span> hic_matrix </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">14</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">15</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[tads] </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">16</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file <span class="cm-operator">=</span> <span class="cm-comment"># path/to/specific/{outprefix}_domains.bed from hicFindTADs of hic matrix file.</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">17</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file_type <span class="cm-operator">=</span> domains</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">18</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">border_color <span class="cm-operator">=</span> black </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">19</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">color <span class="cm-operator">=</span> none </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">20</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># the tads are overlay over the hic-matrix </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">21</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># the share-y options sets the y-axis to be shared </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">22</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># between the Hi-C matrix and the TADs. </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">23</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">overlay_previous <span class="cm-operator">=</span> share-y </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">24</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">25</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[bedgraph] </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">26</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file <span class="cm-operator">=</span> <span class="cm-comment"># path/to/specific/{outprefix}_score.bedgraph from hicFindTADs of hic matrix file.</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">27</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">color <span class="cm-operator">=</span> blue </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">28</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">height <span class="cm-operator">=</span> <span class="cm-number">3</span> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">29</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">title <span class="cm-operator">=</span> TAD score </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">30</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">max_value <span class="cm-operator">=</span> <span class="cm-number">10</span> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">31</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">32</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[spacer] </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">33</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">height <span class="cm-operator">=</span> <span class="cm-number">1</span> </span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 525px;"></div><div class="CodeMirror-gutters" style="height: 525px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 34px;"></div></div></div></div></pre><p><span>Il est donc nécessaire de réaliser un fichier </span><code>tracks.ini</code><span> par plot que l'on souhaite réaliser. </span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/tads/offspring_25000.png" referrerpolicy="no-referrer"></p><p><span>Il est aussi possible de mettre les plots directement les uns en dessous des autres par exemple :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash" style="break-inside: unset;"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 50.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 37px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>43</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -37px; width: 37px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[x-axis]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-def">fontsize</span><span class="cm-operator">=</span><span class="cm-number">10</span> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[hic matrix] </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file <span class="cm-operator">=</span> hdf5/file1_corrected.h5</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">title <span class="cm-operator">=</span> File1 <span class="cm-number">25000</span> bins</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># depth is the maximum distance plotted in bp. In Hi-C tracks </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># the height of the track is calculated based on the depth such </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># that the matrix does not look deformed </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">10</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">colormap <span class="cm-operator">=</span> Spectral_r </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">11</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">depth <span class="cm-operator">=</span> <span class="cm-number">1500000</span> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">12</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">transform <span class="cm-operator">=</span> log1p </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">13</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file_type <span class="cm-operator">=</span> hic_matrix </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">14</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">15</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[tads] </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">16</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file <span class="cm-operator">=</span> TADs/file1_domains.bed</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">17</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file_type <span class="cm-operator">=</span> domains</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">18</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">border_color <span class="cm-operator">=</span> black </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">19</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">color <span class="cm-operator">=</span> none </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">20</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># the tads are overlay over the hic-matrix </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">21</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># the share-y options sets the y-axis to be shared </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">22</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># between the Hi-C matrix and the TADs. </span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">23</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">overlay_previous <span class="cm-operator">=</span> share-y </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">24</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">25</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[spacer]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">26</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">height <span class="cm-operator">=</span> <span class="cm-number">1</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">27</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">28</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[hic matrix] </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">29</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file <span class="cm-operator">=</span> hdf5/file2_corrected.h5</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">30</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">title <span class="cm-operator">=</span> File2 <span class="cm-number">25000</span> bins</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">31</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">colormap <span class="cm-operator">=</span> Spectral_r </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">32</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">depth <span class="cm-operator">=</span> <span class="cm-number">1500000</span> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">33</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">transform <span class="cm-operator">=</span> log1p </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">34</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file_type <span class="cm-operator">=</span> hic_matrix </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">35</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">36</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[tads] </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">37</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file <span class="cm-operator">=</span> TADs/file2_domains.bed</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">38</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">file_type <span class="cm-operator">=</span> domains</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">39</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">border_color <span class="cm-operator">=</span> black </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">40</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">color <span class="cm-operator">=</span> none </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">41</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">overlay_previous <span class="cm-operator">=</span> share-y </span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">42</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">43</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">...</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 645px;"></div><div class="CodeMirror-gutters" style="height: 645px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 34px;"></div></div></div></div></pre><p><span>Ici par exemple, les résultats du trio1 à la résolution 25.000 bins ont été assemblés dans le même fichier .jpg :</span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/tads/Full_25k_1M-3M.png" referrerpolicy="no-referrer"></p><p><span>Il est alors possible d'observer que le TAD entre 1.15 et 1.75 chez mother et offspring se trouve découper en deux chez le père. Une approche génomique pourrait éventuellement montrer un évenement d'indel à ce niveau expliquant la différence de TAD-separation score.</span></p><h1><a name="snakemake-et-automatisation" class="md-header-anchor"></a><span>Snakemake et automatisation</span></h1><p><span>Une fois la partie technique réalisée, il a fallut concentrer les efforts sur la mise en place d'une pipeline permettant la répétabilité, la reproductibilité, la portabilité et l'automatisation des analyses effectuer.</span></p><p><span>Snakemake est un gestionnaire de pipeline, issue de python et de GNU Make. Il est basé sur un système de "règles" (rules) qui possède un ou plusieurs input, et qui retourne au moins un output. Cet output peut être le produit final, comme un intermédiaire qui devient un input dans la règle suivante.</span></p><p><span>Par exemple, voici le DAG des étapes hicExplorer sur trio1.offspring, à la résolution 25.000 bins pour 3 régions d'intérêt :</span></p><p><img src="/home/jeremy/Bureau/polledHiC/images/dag.png" referrerpolicy="no-referrer"></p><p><span>Il est donc possible de décomposer l'intégralité des travaux réalisés en deux grandes étapes :</span></p><ul><li><span>nfcore-hic : pour traiter les données de séquençage et obtenir les matrices de contacts.</span></li><li><span>hicexplorer : pour traiter les matrices de contacts et obtenir les carte HiC et plotTADs</span></li></ul><h2><a name="nfcore-hic" class="md-header-anchor"></a><span>nfcore-hic</span></h2><p><span>Après plusieurs tentatives pour intégrer le nextflow dans le Snakemake, il a été convenu de garder séparer les deux workflows. Le dossier nfcore-hic contient deux fichier : </span><strong><span>nfcore-hic.config</span></strong><span> et </span><strong><span>nfcore-hic.sh</span></strong><span>.</span></p><h3><a name="nfcore-hicconfig" class="md-header-anchor"></a><span>nfcore-hic.config</span></h3><p><span>Le fichier </span><code>nfcore-hic.config</code><span> contient les règles d'utilisation en temps et mémoire de certains sous-jobs pour la soumission sur le cluster. </span><strong><span>Il n'est pas nécessaire de le modifier.</span></strong></p><h3><a name="nfcore-hicsh" class="md-header-anchor"></a><span>nfcore-hic.sh</span></h3><p><span>Le fichier </span><code>nfcore-hic.sh</code><span> est le script permettant d'initier l'espace de travail. Ce dernier </span><strong><span>ne soumet pas le job sur le cluster</span></strong><span>.</span></p><p><span>Il est nécessaire de personnaliser ce fichier, notamment les parties </span><strong><span>Set parametres</span></strong><span>, </span><strong><span>Set restriction/ligation parametres</span></strong><span> et </span><strong><span>--bin-size</span></strong><span> :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>9</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Set parametres :</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-def">datadir</span><span class="cm-operator">=</span> <span class="cm-comment"># path/to/reads_directories i.e. : /work2/genphyse/dynagen/jmartin/polledHiC/data/reads_nfcore</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-def">wdir</span><span class="cm-operator">=</span> <span class="cm-comment"># path/to/working_directory i.e. : /work2/genphyse/dynagen/jmartin/polledHiC/workflows/nfcorehic_jm</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-def">genome</span><span class="cm-operator">=</span> <span class="cm-comment"># path/to/genomic_bank i.e. : /bank/bowtie2db/ensembl_bos_taurus_genome</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-def">chromsize</span><span class="cm-operator">=</span> <span class="cm-comment"># path/to/chrom.lengh file i.e. : /work2/genphyse/dynagen/jmartin/polledHiC/data/genome/chrom.len</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 180px;"></div><div class="CodeMirror-gutters" style="height: 180px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>Lors de l'utilisation du pipeline, l'architecture du répertoire data était la suivante </span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang=""><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang=""><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 50.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 37px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>12</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -37px; width: 37px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">├── polledHiC</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">│ ├── data</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | ├── reads_nfcore</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | ├── Arima</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | | ├── trio1.mother.run1.Arima...fastq.gz</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | | ├── trio1.mother.run2.Arima...fastq.gz</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | | ├── trio1.offspring.run1.Arima...fastq.gz</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | | └── ...</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | ├── Dovetail</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">10</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | | └── ...</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">11</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | └── ...</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">12</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | └── genome</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 180px;"></div><div class="CodeMirror-gutters" style="height: 180px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 34px;"></div></div></div></div></pre><p><span>Dans la seconde partie, il est nécessaire de modifier le case </span><code>[protocol]</code><span> et renseigner les fragments de restriction et ligations :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 50.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 37px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>13</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -37px; width: 37px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-comment"># Set restriction/ligation parametres</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> case <span class="cm-def">$prot</span> <span class="cm-keyword">in</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> *[protocol]) <span class="cm-def">restriction</span><span class="cm-operator">=</span> <span class="cm-comment"># restriction fragment as following : '^GATC,G^ANTC'</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-def">ligation</span><span class="cm-operator">=</span> <span class="cm-comment"># ligation fragment as following : 'GATCGATC,GANTGATC,GANTANTC,GATCANTC'</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-builtin">echo</span> <span class="cm-string">"run [protocol] : </span><span class="cm-def">$run</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-string"> res : </span><span class="cm-def">$restriction</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-string"> lig : </span><span class="cm-def">$ligation</span><span class="cm-string">"</span>;;</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> *) <span class="cm-def">restriction</span><span class="cm-operator">=</span><span class="cm-string">'not recognized'</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-def">ligation</span><span class="cm-operator">=</span><span class="cm-string">'not recognized'</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">10</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-builtin">echo</span> <span class="cm-string">"run NOT RECOGNIZED : </span><span class="cm-def">$run</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">11</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-string"> res : </span><span class="cm-def">$restriction</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">12</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-string"> lig : </span><span class="cm-def">$ligation</span><span class="cm-string">"</span>;;</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">13</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"> <span class="cm-keyword">esac</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 225px;"></div><div class="CodeMirror-gutters" style="height: 225px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 34px;"></div></div></div></div></pre><p><span>Si il n'y a qu'un seul protocole à étudier, il est alors possible de remplacer le </span><code>case</code><span> par :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>6</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Set restriction/ligation paramtres</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-def">restriction</span><span class="cm-operator">=</span> <span class="cm-comment"># restriction fragment as following: '^GATC,G^ANTC'</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-def">ligation</span><span class="cm-operator">=</span> <span class="cm-comment"># ligation fragment as following: 'GATCGATC,GANTGATC,GANTANTC,GATCANTC'</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-builtin">echo</span> <span class="cm-string">"run [protocol] : </span><span class="cm-def">$run</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-string">res : </span><span class="cm-def">$restriction</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-string">lig : </span><span class="cm-def">$ligation</span><span class="cm-string">"</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 90px;"></div><div class="CodeMirror-gutters" style="height: 90px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>Enfin, la ligne --bin-size contient les différentes résolutions d'études. Il est important de respecter la typologie d'écriture :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash" style="break-inside: unset;"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 50.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 37px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>16</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -37px; width: 37px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">65</span> <span class="cm-comment"># most are default options - skipping ICE because normalizing</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">66</span> <span class="cm-comment"># each technical replicate is not relevant</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">67</span> nextflow run nf-core/hic \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">68</span> <span class="cm-attribute">-revision</span> <span class="cm-number">1</span>.1.0 \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">69</span> <span class="cm-attribute">-profile</span> genotoul \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">70</span> <span class="cm-attribute">-name</span> <span class="cm-string">'$runid'</span> \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">71</span> <span class="cm-attribute">-c</span> <span class="cm-string">'"'"</span><span class="cm-def">$conf</span><span class="cm-string">"'"'</span> \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[...]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">77</span> <span class="cm-attribute">--reads</span> <span class="cm-string">'"'"''</span><span class="cm-def">$readsdir</span><span class="cm-string">'/*_R{1,2}.fastq.gz'"'"'</span> \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">10</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[...]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">11</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">81</span> <span class="cm-attribute">--restriction_site</span> <span class="cm-string">'"'"</span><span class="cm-def">$restriction</span><span class="cm-string">"'"'</span> \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">12</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">82</span> <span class="cm-attribute">--ligation_site</span> <span class="cm-string">'"'"</span><span class="cm-def">$ligation</span><span class="cm-string">"'"'</span> \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">13</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[...]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">14</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">88</span> <span class="cm-attribute">--bin_size</span> <span class="cm-comment"># remplace x,y,z as following : '"'"'x,y,z'"'"' \</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">15</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">[...]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">16</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">94</span> <span class="cm-attribute">--skipCool</span><span class="cm-string">' > $script</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 240px;"></div><div class="CodeMirror-gutters" style="height: 240px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 34px;"></div></div></div></div></pre><p><span>Par exemple, dans le cadre de l'étude réalisé, cette ligne contenais :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>1</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">88</span> <span class="cm-attribute">--bin-size</span> <span class="cm-string">'"'"'200000,50000,25000,10000'"'"'</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 15px;"></div><div class="CodeMirror-gutters" style="height: 15px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>Une fois ce script exécuté, dans chaque sous répertoires se trouvera un script permettant de soumettre le job sur le cluster :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash" style="break-inside: unset;"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 50.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 37px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>15</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -37px; width: 37px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">├── polledHiC</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">│ ├── nfcore-hic</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | ├── Arima</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | └── Arima.sh</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | ├── Dovetail</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | └── Dovetail.sh</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | ├── Maison</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | | └── Maison.sh</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | |</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">10</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | ├── nfcore-hic.config</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">11</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | |</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">12</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">| | └── nfcore-hic.sh</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">13</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">14</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Exemple de soumission :</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">15</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">sbatch nfcore-hic/Arima/Arima.sh</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 225px;"></div><div class="CodeMirror-gutters" style="height: 225px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 34px;"></div></div></div></div></pre><h2><a name="hicexplorer-n4201" class="md-header-anchor"></a><span>hicexplorer</span></h2><p><span>Pour pouvoir executer le pipeline, il est essentiel d'avoir activer l'environnement </span><a href='#conda--polledhicenv'><strong><span>polledHiC_env</span></strong></a><span>.</span></p><p><span>Le répertoire hicexplorer contient quatre fichiers :</span></p><ul><li><span>config.yaml</span></li><li><span>make_sampled_protocol.py</span></li><li><span>Snakefile</span></li><li><span>hicexplorer.sh</span></li></ul><h3><a name="configyaml" class="md-header-anchor"></a><span>config.yaml</span></h3><p><span>Fichier de configuration du Snakefile. Il est nécessaire de le personnaliser quasi-entièrement pour correspondre aux analyses souhaitées.</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="python"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="python"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 50.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 37px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>13</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -37px; width: 37px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment">### Config.yaml to set wildcards to Snakefile ###</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">workdir</span>: <span class="cm-comment"># path/to/working_directory</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">sampled_protocols</span>: <span class="cm-variable">sampled_protocols</span>.<span class="cm-property">tsv</span> <span class="cm-comment"># don't edit this line !</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">resolutions</span>: <span class="cm-comment"># resolution of interest</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">chromosomes</span>: <span class="cm-comment"># full chromosomes to adjust without contig</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">10</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">11</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">regions</span>: <span class="cm-comment"># regions of interest</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">12</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">13</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">samples</span>: <span class="cm-comment"># samples who matched with sample column of sampled_protocols</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 195px;"></div><div class="CodeMirror-gutters" style="height: 195px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 34px;"></div></div></div></div></pre><p><em><span>i.e.</span></em><span> : le config.yaml utilisé pendant ce projet </span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded md-focus" lang="python"><div class="CodeMirror cm-s-inner CodeMirror-wrap CodeMirror-focused" lang="python"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 50.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 37px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>13</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -37px; width: 37px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment">### Config.yaml to set wildcards to Snakefile ###</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">workdir</span>: <span class="cm-operator">/</span><span class="cm-variable">home</span><span class="cm-operator">/</span><span class="cm-variable">user</span><span class="cm-operator">/</span><span class="cm-variable">polledHiC</span><span class="cm-operator">/</span><span class="cm-variable">workflows</span><span class="cm-operator">/</span><span class="cm-variable">hicexplorer</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">sampled_protocols</span>: <span class="cm-variable">sampled_protocols</span>.<span class="cm-property">tsv</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">resolutions</span>: [<span class="cm-number">200000</span>,<span class="cm-number">50000</span>,<span class="cm-number">25000</span>,<span class="cm-number">10000</span>]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">chromosomes</span>: [<span class="cm-number">1</span>, <span class="cm-number">2</span>, <span class="cm-number">3</span>, <span class="cm-number">4</span>, <span class="cm-number">5</span>, <span class="cm-number">6</span>, <span class="cm-number">7</span>, <span class="cm-number">8</span>, <span class="cm-number">9</span>, <span class="cm-number">10</span>, <span class="cm-number">11</span>, <span class="cm-number">12</span>, <span class="cm-number">13</span>, <span class="cm-number">14</span>, <span class="cm-number">15</span>, <span class="cm-number">16</span>, <span class="cm-number">17</span>, <span class="cm-number">18</span>, <span class="cm-number">19</span>, <span class="cm-number">20</span>, <span class="cm-number">21</span>, <span class="cm-number">22</span>, <span class="cm-number">23</span>, <span class="cm-number">24</span>, <span class="cm-number">25</span>, <span class="cm-number">26</span>, <span class="cm-number">27</span>, <span class="cm-number">28</span>, <span class="cm-number">29</span>, <span class="cm-variable">X</span>]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">10</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">11</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">regions</span>: [<span class="cm-string">'1-158534110'</span>, <span class="cm-string">'1000000-6000000'</span>, <span class="cm-string">'1000000-3000000'</span>, <span class="cm-string">'1500000-3500000'</span>, <span class="cm-string">'2000000-3000000'</span>, <span class="cm-string">'2200000-2800000'</span>]</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">12</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">13</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-variable">samples</span>: [<span class="cm-variable">trio1</span>.<span class="cm-property">offspring</span>, <span class="cm-variable">trio1</span>.<span class="cm-property">father</span>, <span class="cm-variable">trio1</span>.<span class="cm-property">mother</span>, <span class="cm-variable">trio2</span>.<span class="cm-property">offspring</span>, <span class="cm-variable">trio2</span>.<span class="cm-property">mother</span>, <span class="cm-variable">trio2</span>.<span class="cm-property">father</span>]</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 240px;"></div><div class="CodeMirror-gutters" style="height: 240px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 34px;"></div></div></div></div></pre><h3><a name="makesampledprotocolpy" class="md-header-anchor"></a><span>make_sampled_protocol.py</span></h3><p><span>Ce script permet d'initier la création d'un fichier tabulé contenant les informations des différentes matrices de contact à traiter.</span></p><p><span>Il est nécessaire de renseigner la ligne 19 :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="python"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="python"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>1</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">19</span> <span class="cm-variable">nfcore_dir</span> = <span class="cm-comment"># 'path/to/nfcore_directory/*/' <- the '/*/' at the end allow to only return directory with glob.</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 30px;"></div><div class="CodeMirror-gutters" style="height: 30px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><em><span>i.e.</span></em><span> : le script utilisé pour l'analyse :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="python"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="python"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>1</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation"><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">19</span> <span class="cm-variable">nfcore_dir</span> = <span class="cm-string">'/home/user/polledHiC/workflows/nfcore-hic/*/'</span></span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 15px;"></div><div class="CodeMirror-gutters" style="height: 15px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><h3><a name="snakefile" class="md-header-anchor"></a><span>Snakefile</span></h3><p><span>Le Snakefile est le fichier contenant toutes les règles d’exécution du snakemake. Ici non plus il n'y a pas de modification à apporter.</span></p><p><span>Le Snakefile contient 12 règles (ou 'rules') pour mener de bout en bout le pipeline d'analyse.</span></p><p><span>Il est appelée par le script hicexplorer.sh pour être lancer comme un job sur le cluster genologin. Il est toutefois possible de lancer un dry-run sur une session dédiée :</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 50.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 37px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>11</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -37px; width: 37px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Demande d'une session dédiée :</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">srun <span class="cm-attribute">-c</span> <span class="cm-number">1</span> <span class="cm-attribute">--mem</span><span class="cm-operator">=</span>8G <span class="cm-attribute">--pty</span> <span class="cm-builtin">bash</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Activation de l'environnement conda si ce n'est pas déjà fait :</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">conda activate polledHiC</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Dry-run :</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">snakemake <span class="cm-attribute">-j</span> <span class="cm-number">1</span> <span class="cm-attribute">-p</span> <span class="cm-attribute">-n</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 26px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">10</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># Plot du DAG en prenant en compte les informations du config.yaml :</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -37px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 26px;">11</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;">snakemake <span class="cm-attribute">--dag</span> | dot <span class="cm-attribute">-Tpng</span> <span class="cm-attribute">-o</span> dag.png</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 165px;"></div><div class="CodeMirror-gutters" style="height: 165px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 34px;"></div></div></div></div></pre><h3><a name="hicexplorersh" class="md-header-anchor"></a><span>hicexplorer.sh</span></h3><p><span>Le script hicexplorer.sh permet de soumettre l'analyse sur le cluster.</span></p><p><span>Par défaut, le Snakefile est paramétré pour réaliser un </span><code>dry-run</code><span>. Ce dernier liste les différentes étapes que va réaliser snakemake, sans les réaliser.</span></p><p><span>Cela permet d'avoir une première vision et de s'assurer que tout les fichiers de configurations soient correctement renseignés.</span></p><p><span>Si le dry-run s'exécute correctement, il suffit d'enlever l'option </span><code>-n</code><span> à la commande snakemake</span></p><pre spellcheck="false" class="md-fences md-end-block md-fences-with-lineno ty-contain-cm modeLoaded" lang="bash"><div class="CodeMirror cm-s-inner CodeMirror-wrap" lang="bash"><div style="overflow: hidden; position: relative; width: 3px; height: 0px; top: 7.5px; left: 42.5px;"><textarea autocorrect="off" autocapitalize="off" spellcheck="false" tabindex="0" style="position: absolute; bottom: -1em; padding: 0px; width: 1000px; height: 1em; outline: none;"></textarea></div><div class="CodeMirror-scrollbar-filler" cm-not-content="true"></div><div class="CodeMirror-gutter-filler" cm-not-content="true"></div><div class="CodeMirror-scroll" tabindex="-1"><div class="CodeMirror-sizer" style="margin-left: 29px; margin-bottom: 0px; border-right-width: 0px; padding-right: 0px; padding-bottom: 0px;"><div style="position: relative; top: 0px;"><div class="CodeMirror-lines" role="presentation"><div role="presentation" style="position: relative; outline: none;"><div class="CodeMirror-measure"><pre><span>xxxxxxxxxx</span></pre><div class="CodeMirror-linenumber CodeMirror-gutter-elt"><div>9</div></div></div><div class="CodeMirror-measure"></div><div style="position: relative; z-index: 1;"></div><div class="CodeMirror-code" role="presentation" style=""><div class="CodeMirror-activeline" style="position: relative;"><div class="CodeMirror-activeline-background CodeMirror-linebackground"></div><div class="CodeMirror-gutter-background CodeMirror-activeline-gutter" style="left: -29px; width: 29px;"></div><div class="CodeMirror-gutter-wrapper CodeMirror-activeline-gutter" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">1</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># from</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">2</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">33</span> snakemake <span class="cm-attribute">--jobs</span> <span class="cm-number">1</span> <span class="cm-attribute">-p</span> <span class="cm-attribute">-n</span>\</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">3</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">34</span> <span class="cm-attribute">--snakefile</span> /work2/genphyse/dynagen/jmartin/polledHiC/workflows/hicexplorer_jm/Snakefile \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">4</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">35</span> <span class="cm-attribute">--directory</span> /work2/genphyse/dynagen/jmartin/polledHiC/workflows/hicexplorer_jm/</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">5</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span cm-text=""></span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">6</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-comment"># to</span></span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">7</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">33</span> snakemake <span class="cm-attribute">--jobs</span> <span class="cm-number">1</span> <span class="cm-attribute">-p</span> \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt" style="left: 2px; width: 18px;">8</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">34</span> <span class="cm-attribute">--snakefile</span> /work2/genphyse/dynagen/jmartin/polledHiC/workflows/hicexplorer_jm/Snakefile \</span></pre></div><div style="position: relative;"><div class="CodeMirror-gutter-wrapper" style="left: -29px;"><div class="CodeMirror-linenumber CodeMirror-gutter-elt CodeMirror-linenumber-show" style="left: 2px; width: 18px;">9</div></div><pre class=" CodeMirror-line " role="presentation"><span role="presentation" style="padding-right: 0.1px;"><span class="cm-number">35</span> <span class="cm-attribute">--directory</span> /work2/genphyse/dynagen/jmartin/polledHiC/workflows/hicexplorer_jm/</span></pre></div></div></div></div></div></div><div style="position: absolute; height: 0px; width: 1px; border-bottom: 0px solid transparent; top: 195px;"></div><div class="CodeMirror-gutters" style="height: 195px;"><div class="CodeMirror-gutter CodeMirror-linenumbers" style="width: 26px;"></div></div></div></div></pre><p><span>Libre à vous de vouloir ou non laisser s'exécuter la création d'un </span><strong><span>"consensus"</span></strong><span> en dé-commentant les lignes 40 à 70.</span></p><p><span>Attention, si ces lignes sont dé-commenter lors du dry-run, le job sera en erreur sur le cluster, étant donnée que le snakemake ne ce sera pas exécuter, il n'y aura aucune matrice à sommer.</span></p><h1><a name="tldr--comment-lancer-une-analyse-sur-genologin-" class="md-header-anchor"></a><span>TL;DR : Comment lancer une analyse sur Genologin :</span></h1><ul><li><p><span>NFCore-hic :</span></p><ol start='' ><li><span>Télécharger les reads au format fastq.gz dans des repertoirs distincts </span><code>data/reads/Protocol</code></li><li><span>Renseigner les champs du fichier </span><code>nfcore-hic/nfcore-hic.sh</code><span>.</span></li><li><span>Executer </span><code>sh nfcore-hic/nfcore-hic.sh</code><span>.</span></li><li><span>Soummettre le job </span><code>sbatch nfcore-hic/Protocol/Protocol.sh</code></li></ol></li></ul><p><span>Puis une fois le nextflow terminé ;</span></p><ul><li><p><span>hicExplorer :</span></p><ol start='4' ><li><span>Renseigner les champs du fichier </span><code>hicexplorer/config.yaml</code></li><li><span>Renseigner le chemin des matrices dans </span><code>hicexplorer/make_sampled_protocol.py</code></li><li><span>Réaliser un dry-run en exécutant : </span><code>sankemake -j 1 -p -n</code><span> dans le dossier </span><code>hicexplorer</code></li><li><span>Enlevé le </span><code>-n</code><span> à la ligne 33 de </span><code>hicexplorer.sh</code></li><li><span>Soumettre l'analyse </span><code>sbatch hicexplorer.sh</code></li></ol></li></ul><p> </p><p> </p></div>
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