macs2
Link to section 'Introduction' of 'macs2' Introduction
MACS2
is Model-based Analysis of ChIP-Seq for identifying transcript factor binding sites.
MACS consists of four steps:
- removing redundant reads
- adjusting read position
- calculating peak enrichment
- estimating the empirical false discovery rate (FDR).
For more information, please check its website: https://biocontainers.pro/tools/macs2 and its home page on Github.
Link to section 'Versions' of 'macs2' Versions
- 2.2.7.1
Link to section 'Commands' of 'macs2' Commands
- macs2
Link to section 'Module' of 'macs2' Module
You can load the modules by:
module load biocontainers
module load macs2
Link to section 'Example job' of 'macs2' 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 MACS2 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=macs2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers macs2
macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01