Scripts from Juicer pipeline for analysis of Hi-C data (https://github.com/aidenlab/juicer) modified for use on Rackham / Uppmax.
The following changes to the original code were made.
juicer_rackham.sh
-
load modules for
bwa
and related available on Rackham; -
remove some of the Aiden lab specific code;
-
add the currect script name
split_rmdups_rackham.awk
in the DEDUP step; modify the call to this script to include CPU allocation; -
correct cmd for DUPCHECK step to include CPU allocation;
split_rmdups_rackham.awk
- correct
sbatch
calls to include CPU allocation;
Clone the repository, copy the scripts to juicer/scripts
and that's it.