cellranger
Cellranger is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Detailed usage can be found here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger.
Link to section 'Versions' of 'cellranger' Versions
- 6.0.1
- 6.1.1
- 6.1.2
- 7.0.0
- 7.0.1
- 7.1.0
Link to section 'Commands' of 'cellranger' Commands
- cellranger mkfastq
- cellranger count
- cellranger aggr
- cellranger reanalyze
- cellranger multi
Link to section 'Module' of 'cellranger' Module
You can load the modules by:
module load biocontainers
module load cellranger
Link to section 'Example job' of 'cellranger' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run cellranger our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 48
#SBATCH --job-name=cellranger
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers cellranger
cellranger count --id=run_count_1kpbmcs --fastqs=pbmc_1k_v3_fastqs --sample=pbmc_1k_v3 --transcriptome=refdata-gex-GRCh38-2020-A