cellranger-atac
Link to section 'Introduction' of 'cellranger-atac' Introduction
Cellranger-atac is a set of analysis pipelines that process Chromium Single Cell ATAC data.
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.
Link to section 'Versions' of 'cellranger-atac' Versions
- 2.0.0
- 2.1.0
Link to section 'Commands' of 'cellranger-atac' Commands
- cellranger-atac
Link to section 'Module' of 'cellranger-atac' Module
You can load the modules by:
module load biocontainers
module load cellranger-atac
Link to section 'Example job' of 'cellranger-atac' 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-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