Purdue University

Commands

• HiC-Pro
• digest_genome.py
• extract_snps.py
• hicpro2fithic.py
• hicpro2higlass.sh
• hicpro2juicebox.sh
• make_viewpoints.py
• sparseToDense.py
• split_reads.py
• split_sparse.py

Module

You can load the modules by:

module load biocontainers
module load hic-pro

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 hic-pro on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hic-pro
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers hic-pro