Cellranger

Introduction

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.

For more information, please check:

DockerHub: https://hub.docker.com/r/cumulusprod/cellranger

Home page: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

Versions

• 7.0.1

• 7.1.0

Commands

• cellranger

Example job

Warning

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 on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=cellranger
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load cellranger/XXXX ### you can run *module avail cellranger* to check all available versions

cellranger count --id=run_count_1kpbmcs --fastqs=pbmc_1k_v3_fastqs --sample=pbmc_1k_v3 --transcriptome=refdata-gex-GRCh38-2020-A