aakashsur/hic-qc repository overview

⁠Hi-C QC in Docker

Phase Genomics⁠ has a rich Hi-C quality control report. This is a containerization of hic_qc.py⁠ and it is publically available via Docker Hub. To leave issues, visit the repository⁠.

⁠Usage

docker pull \
  aakashsur/hic_qc

docker run \
  --rm \
  --volume $PWD:/root/results \
  --workdir /root/results \
  aakashsur/hic-qc \
  hic-qc \
  -b alignment.bam

⁠Details

The hic-qc command has been placed in $PATH. Easiest way to run is to have everything in $PWD, i.e. the name sorted .bam file. The current local directory then gets mounted to a folder in the home directory of the container, which is /root/results. To get the options for hic-qc simply run docker run --rm aakashsur/hic-qc hic-qc --help.

For running in an HPC setting, where singularity is often the choice of containerization -

singularity pull 
  docker://aakashsur/hic-qc
  
singularity run \
    --bind $PWD:/root/results/ \
    --workdir /root/results \
    hic-qc_latest.sif \
    hic-qc \
    -b alignment.bam