Software: Genrich
Description
Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.
Available Versions
| Unspecified: | 0.6.1 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/genrich and its home page on Github.
Commands
- Genrich
Module
You can load the modules by:
module load biocontainers
module load genrich
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run Genrich on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=genrich
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers genrich
Genrich -t sample.bam -o sample.narrowPeak -v