cellranger-atac.rst

Cellranger-atac

Introduction ~~~~~~~~ Cellranger-atac is a set of analysis pipelines that process Chromium Single Cell ATAC data.

For more information, please check its | Docker hub: https://hub.docker.com/r/cumulusprod/cellranger-atac and its home page: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/algorithms/overview.

Versions

• 2.0.0
• 2.1.0

Commands ~~~~~~~ - cellranger-atac

Module

You can load the modules by:

module load biocontainers
module load cellranger-atac

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-atac on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --mem=64G
#SBATCH --job-name=cellranger-atac
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cellranger-atac

cellranger-atac count --id=sample345 \
                    --reference=refdata-cellranger-arc-GRCh38-2020-A-2.0.0 \
                    --fastqs=runs/HAWT7ADXX/outs/fastq_path \
                    --sample=mysample \
                    --localcores=8 \
                    --localmem=64