https://github.com/cellgeni/various_cellrangers
Various Cellranger Scripts used for different version etc
https://github.com/cellgeni/various_cellrangers
Last synced: 4 months ago
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Various Cellranger Scripts used for different version etc
- Host: GitHub
- URL: https://github.com/cellgeni/various_cellrangers
- Owner: cellgeni
- License: mit
- Created: 2023-04-19T14:58:27.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2025-03-27T14:59:59.000Z (about 1 year ago)
- Last Synced: 2025-12-27T11:28:13.139Z (5 months ago)
- Language: Shell
- Size: 11.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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 `_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.