cellranger-arc
Link to section 'Introduction' of 'cellranger-arc' Introduction
Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression (GEX), chromatin accessibility, and their linkage. Furthermore, since the ATAC and GEX measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and GEX.
Docker hub: https://hub.docker.com/r/cumulusprod/cellranger-arc
Home page: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
Link to section 'Versions' of 'cellranger-arc' Versions
- 2.0.2_patched
- 2.0.2
Link to section 'Commands' of 'cellranger-arc' Commands
- cellranger-arc
Link to section 'Module' of 'cellranger-arc' Module
You can load the modules by:
module load biocontainers
module load cellranger-arc
Link to section 'Example job' of 'cellranger-arc' 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-arc on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cellranger-arc
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers cellranger-arc