This script is intended as a simple QC method for Hi-C libraries, based on reads in a BAM file aligned to some genome/assembly.

• Version: git-1e132fb2
• Added: November, 2020
• Link: https://github.com/phasegenomics/hic_qc

See versions of hic_qc that are available:

$ module avail hic_qc

Load one version into your environment and run it:

$ module load hic_qc/git-1e132fb2
$ hic_qc.py

Notes from the sysadmin during installation.

$ cd /tmp
$ git clone https://github.com/phasegenomics/hic_qc.git
$ cd hic_qc
$ sudo mkdir -p /export/apps/hic_qc/git-1e132fb2
$ sudo chown aorth /export/apps/hic_qc/git-1e132fb2
$ python3 -m venv /export/apps/hic_qc/git-1e132fb2
$ source /export/apps/hic_qc/git-1e132fb2/bin/activate
$ pip install -r requirements.txt
$ python setup.py install
$ cp -r * /export/apps/hic_qc/git-1e132fb2
$ sudo chown -R root:root /export/apps/hic_qc/git-1e132fb2