Cellranger Scripts

This is a repository containing various Cellranger scripts used for different protocols etc. Each script should use the same submission script with the sample file structured the same way.

Cellranger FASTQ naming convention

Cellranger expects FASTQ files to be formatted in a particular manner, they should look like <SAMPLEID>_S*_L00*_R[1|2]_001.fastq.gz.

Common Practices

• sample.list - This is a file with a different sample per line. Each line is tab-separated containing a SAMPLEID followed by an absolute path to directory containing fastqs. The SAMPLEID should be the entire name of the FASTQ files for that sample prior to _S*_L00*_R[1|2]_001.fastq.gz
• submit_cellranger.sh - This is a submission script which submits cellranger to a job on the FARM.

Submitting Cellranger

Cellranger is submitted from the command line as followed:

cat sample.list | while read sample fqdir; do /path/to/submit_cellranger.sh /path/to/cellranger_script.sh $sample $fqdir; done

Different versions of cellranger

Each example script here is for a specific version of cellranger (the one used in the request the script was taken from).

If you want a different version replace, check if the version you need is installed inside /software/cellgeni, if it is replace /software/cellgeni/cellranger-version with your desired version.

If it is not installed reach out to the team in order to get it installed there.