genrich
Link to section 'Introduction' of 'genrich' Introduction
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.
For more information, please check its website: https://biocontainers.pro/tools/genrich and its home page on Github.
Link to section 'Versions' of 'genrich' Versions
- 0.6.1
Link to section 'Commands' of 'genrich' Commands
- Genrich
Link to section 'Module' of 'genrich' Module
You can load the modules by:
module load biocontainers
module load genrich
Link to section 'Example job' of 'genrich' 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 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