Hic-pro
Introduction
Hicpro is an optimized and flexible pipeline for Hi-C data processing.
For more information, please check:
Docker hub: https://hub.docker.com/r/nservant/hicpro
Home page: https://github.com/nservant/HiC-Pro
Versions
3.0.0
3.1.0
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
Warning
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