epic2 is an ultraperformant reimplementation of SICER. It focuses on speed, low memory overhead and ease of use. It also contains a reimplementation of the SICER-df scripts for differential enrichment and a script to create many kinds of bigwigs from your data.

Features:

• easy to install and use
• reads sam, single-end bam, bed and bedpe (.gz)
• extremely fast
• very low memory requirements
• works both with and without input
• metadata for ~80 UCSC genomes built in
• easily use custom genomes and assemblies with --chromsizes and --effective-genome-fraction args
• differential enrichment for WT vs. KO works with and without input (epic2-df)
• fixes two bugs in the original SICER and one bug in epic
• create many types of useful bigwigs for visualization in genome browsers

https://github.com/biocore-ntnu/epic2

• Module Name: epic2 (see the modules page for more information)
• Example files are under /usr/local/apps/epic2/examples

Allocate an interactive session and run the interactive job there.

[biowulf]$ sinteractive  --mem=5g
salloc.exe: Granted job allocation 789523
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0135 are ready for job

[cn0135]$ cd /data/$USER/

[cn0135]$ module load epic2

[cn0135]$ epic2 -ex
# An example of command can be copied from the output.
[cn0135]$ epic2 -t /opt/conda/envs/app/lib/python3.7/site-packages/epic2/examples/test.bed.gz \
-c /opt/conda/envs/app/lib/python3.7/site-packages/epic2/examples/control.bed.gz > deleteme.txt

[cn0135]$ exit
salloc.exe: Job allocation 789523 has been revoked.

[biowulf]$

1. Create a script file (myscript) similar to the one below

#! /bin/bash
# myscript
set -e

module load epic2 || exit 1
cd /data/$USER/
epic2 -t /opt/conda/envs/app/lib/python3.7/site-packages/epic2/examples/test.bed.gz \
-c /opt/conda/envs/app/lib/python3.7/site-packages/epic2/examples/control.bed.gz > deleteme.txt

2. Submit the script on biowulf:

[biowulf]$ sbatch --mem=5g myscript

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile).

cd /data/$USER/dir1; epic2 ...
cd /data/$USER/dir2; epic2 ...
cd /data/$USER/dir3; epic2 ...
...
cd /data/$USER/dir20; epic2 ...

submit the swarm job:

$ swarm -f cmdfile --module epic2 -g 5

For more information regarding running swarm, see swarm.html