Cellranger-atac

Introduction

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

For more information, please check:

BioContainers: https://biocontainers.pro/tools/cellranger-atac

Home page: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/algorithms/overview

Versions

• 2.0.0

• 2.1.0

Commands

• 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 -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-atac
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

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

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