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Copy pathMISOSetting_burgeSE.mm9.pe200_20.shvar.template
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MISOSetting_burgeSE.mm9.pe200_20.shvar.template
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genome=mm9 ###
typeAnno=burge ###
#MISOPATH=/lab/jaenisch_albert/Apps/yarden/MixtureIsoforms/
#MISOPATH=/lab/jaenisch_albert/bin/newMISO/MISO/
genomeRootDir=/lab/jaenisch_albert/genomes/
genomeSizes=${genomeRootDir}/${genome}/${genome}_nr.sizes
#eventGff=/lab/jaenisch_albert/genomes/mm9/SplidarEventGff/allEvents #####
eventGff=/lab/jaenisch_albert/genomes/mm9/burgeLabEvents/mm9/pickled/SE
#rawGffFile=/lab/jaenisch_albert/genomes/mm9/SplidarEventGff/allEvents.pe.gff #######
rawGffFile=/lab/jaenisch_albert/genomes/mm9/burgeLabEvents/mm9/SE.mm9.gff3
constExonGff=/lab/solexa_jaenisch/jaenisch_albert/genomes/mm9/burgeLabEvents/const_exons/exons.chrSN/Mus_musculus.NCBIM37.65.chrSN.min_1000.const_exons.gff
targetBamFileBaseName=accepted_hits.sorted.bam ### use the sorted one?
readLen=100 ###
pairedEndFlag="--paired-end 200 20" #mean sd
clusterFlag="--use-cluster --chunk-jobs 600" #fastmiso no more using these flags?? --use-cluster --chunk-jobs 1000
bamFileSubRoot=tophatOutput
MISOOutSubRoot=MISOOnPE_burgeSE
misoRunSetting=miso_settings_burgeEvents.txt
splidarEventTypes[0]="SE"
splidarEventTypes[1]="MXE"
splidarEventTypes[2]="RI"
splidarEventTypes[3]="A5SS"
splidarEventTypes[4]="A3SS"
splidarEventTypes[5]="AFE"
splidarEventTypes[6]="ALE"
splidarEventTypes[7]="A3UTR"
bfThresholds[0]=5
bfThresholds[1]=20
bfThresholds[2]=100
dPsiCutOffs[0]=0.1
dPsiCutOffs[1]=0.2
dPsiCutOffs[2]=0.3
dPsiCutOffs[3]=0.5