PePr is a ChIP-Seq Peak-calling and Prioritization pipeline that uses a sliding window approach and models read counts across replicates and between groups with a negative binomial distribution. PePr empirically estimates the optimal shift/fragment size and sliding window width, and estimates dispersion from the local genomic area. Regions with less variability across replicates are ranked more favorably than regions with greater variability. Optional post-processing steps are also made available to filter out peaks not exhibiting the expected shift size and/or to narrow the width of peaks.

References:

• Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA. PePr: A peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics. 2014.

• PePr Main Site: PePr on GitHub

• Module Name: PePr (see the modules page for more information)
• Singlethreaded
• Environment variables set
  • PEPR_EXAMPLES -- path to directory containing simple examples for PePr

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load PePr
[user@cn3144 ~]$ cp $PEPR_EXAMPLES/* .
[user@cn3144 ~]$ PePr -i input_rep1.bed,input_rep2.bed -c chip_rep1.bed,chip_rep2.bed -f bed -s 45 -w 180 -n my_test_run

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. PePr.sh). For example:

#!/bin/bash
module load PePr
PePr -c SRR446029_1.fastq_trim.gz.bam,SRR446030_1.fastq_trim.gz.bam \
  --chip2 SRR446031_1.fastq_trim.gz.bam,SRR446032_1.fastq_trim.gz.bam -f bam --diff -s 10

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] PePr.sh

Create a swarmfile (e.g. PePr.swarm). For example:

PePr -c ex1_A.bam,ex1_B.bam --chip2 ex2_A.bam,ex2_B.bam -f bam --diff -n ex1_ex2
PePr -c ex1_A.bam,ex1_B.bam --chip2 ex3_A.bam,ex3_B.bam -f bam --diff -n ex1_ex3
PePr -c ex1_A.bam,ex1_B.bam --chip2 ex4_A.bam,ex4_B.bam -f bam --diff -n ex1_ex4
PePr -c ex1_A.bam,ex1_B.bam --chip2 ex5_A.bam,ex5_B.bam -f bam --diff -n ex1_ex5

Submit this job using the swarm command.

swarm -f PePr.swarm [-g #] [-t #] --module PePr