juicer-rackham

Scripts from Juicer pipeline for analysis of Hi-C data (https://github.com/aidenlab/juicer) modified for use on Rackham / Uppmax.

Changes

The following changes to the original code were made.

juicer_rackham.sh

1. load modules for bwa and related available on Rackham;

2. remove some of the Aiden lab specific code;

3. add the currect script name split_rmdups_rackham.awk in the DEDUP step; modify the call to this script to include CPU allocation;

4. correct cmd for DUPCHECK step to include CPU allocation;

split_rmdups_rackham.awk

1. correct sbatch calls to include CPU allocation;

Usage

Clone the repository, copy the scripts to juicer/scripts and that's it.