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How to use the COSMIC Database, Enrichr API or local sgRNA re evaluation

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Jan Winter edited this page Mar 29, 2017 · 2 revisions

How to use the COSMIC Database and Enrichr API

COSMIC (Catalogue Of Somatic Mutations In Cancer)

Please note: COSMIC Database access only works in the commmand line installation.

The COSMIC database can be found here. By default, we do not provide the COSMIC database due to licensing compatibility. In case you want to use the COSMIC database, please proceed as follows.

  • Visit the COSMIC Database Website
  • If you aim for a commercial use, please see the COSMIC Licensing Information Page
  • Head to the COSMIC download section
  • Download the COSMIC Mutation Data database file
  • Extract the CosmicMutantExport.tsv.gz file to the a database folder DATABASEFOLDER that you can define on your own
  • Tell CRISPRAnalyzeR during the start that you have an external folder with your database files using the -v parameter -v DATABASEFOLDER:/srv/shiny-server/CRISPRAnalyzeR/database and that you would like to have the COSMIC database included via the parameter -e COSMIC_database="CosmicMutantExport.tsv"

Please replace DATABASEFOLDER byt the full path to the directory where you have placed the CosmicMutantExport.tsv!

docker run --rm -v *DATABASEFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/database -e COSMIC_database="CosmicMutantExport.tsv" -p 80:3838 boutroslab/crispranalyzer:latest

Please note that the COSMIC database is loaded during the analysis procedure and requires 1 GB of RAM.

Enrichr API

Enrichr offers API access for a gene set analysis. By default, CRISPRAnalyzeR has the Enrichr API access ENABLED. You can DISBALE the Enrichr API access during the start by setting the paratemer -e disable_EnrichR=TRUE

 docker run --rm -e disable_EnrichR=TRUE -p 80:3838 boutroslab/crispranalyzer:latest

Please not that you require a license for commercial use. A license can be obtained by contacting the Mount Sinai Technology Development.

More information can be found at the Enrichr Help Page.

How to perform local sgRNA Re-evaluation

Please note: local sgRNA re-evaluation is only supported in the command line installation, not in the Kitematic installation

CRISPRAnalyzeR re-evaluated your sgRNAs during the analysis process. By default, this is done by sending the sgRNAs to www.e-crisp.org and downloading the files again. However, you can also perform a local re-evaluation of your sgRNAs!

You can download the human reference genome (or mus musculus) and tell CRISPRAnalyzeR to perform the re-evaulation locally on your computer. For this, you require at least 60GB of disk space and a pretty fast computer.

Step 1: Download the reference genome
Download the reference genome you need

Step 2: Extract the files to a folder (DATABASEFOLDER) of your desire Extract the downloaded file using gunzip (macOS/Linux) or Zip (Windows) to a DATABASEFOLDER of your desire. Please note that you need to know the exact path to the DATABASEFOLDER! e.g. /home/user1/databases
If you have already setup the COSMIC Database, please make sure you extract the file into that same folder.

Please note: The folder structure MUST be kept, when you extract the file into e.g. /home/user1/databases
this is your DATABASEFOLDER

it will create a folder structure like that:
e.g. /home/user1/databases/data/scripts/crispr_databases/homo_sapiens

Step 3: start CRISPRAnalyzeR and tell it where you files are Using the command line, start CRISPRAnalyzeR and provide the database path DATABASEPATH - so that CRISPRAnalyzeR know where to look for your data.

Please note: if you have setup the COSMIC database already, just extract the files in the same folder and you do not need to do anything in addition

Again, replace DATABASEFOLDER with your absolute path.

docker run --rm -v *DATABASEFOLDER*:/srv/shiny-server/CRISPRAnalyzeR/database -p 80:3838 boutroslab/crispranalyzer:latest
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