PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. The suite contains the following tools:

References:

• X. Feng, R. Grossman and L. Stein. PeakRanger: A cloud-enabled peak caller for ChIP-seq data BMC Bioinformatics 2011, 12:139. PubMed |  PMC |  Journal

• Home page on Sourceforge

• Module Name: peakranger (see the modules page for more information)
• peakranger is a multithreaded application
• Example files in $PEAKRANGER_TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=8g
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 peakranger
[user@cn3144 ~]$ cp -L $PEAKRANGER_TEST_DATA/* .
[user@cn3144 ~]$ ls -lh
-rw-rw-r-- 1 user group 869M Mar  6 14:45 ENCFF374UMR.bam <-- CTCF (GrCh38)
-rw-rw-r-- 1 user group 793M Mar  6 14:46 ENCFF700UBO.bam <-- Control

[user@cn3144 ~]$ peakranger nr --data ENCFF374UMR.bam --control ENCFF700UBO.bam --format bam
...
Estimated noise rate:0.899125

[user@cn3144 ~]$ peakranger wig --format bam --data ENCFF374UMR.bam --output ENCFF374UMR.wig
[user@cn3144 ~]$ # ranger is for narrow peaks
[user@cn3144 ~]$ peakranger ranger --data ENCFF374UMR.bam --control ENCFF700UBO.bam --format bam \
                       --thread 2 --output ENCFF374UMR
Warning: chrEBV only contains reads in the positive strand. The chromosome is removed.
Warning: chrUn_KI270379v1 only contains reads in the negative strand. The chromosome is removed.
Warning: No reads were found in chrEBV of the treatment dataset. The chromosome is removed.
Warning: No reads were found in chrUn_KI270379v1 of the treatment dataset. The chromosome is removed.
[user@cn3144 ~]$ wc -l ENCFF374UMR_region.bed
41305 ENCFF374UMR_region.bed

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

Here is an example of the resulting wig file after conversion to BigWig along with the peak and summit calls (chr1:155,233,328-155,257,703)

Note that the --report option will generate a separate plot for each peak if R is on the path. All the plots will be in a single directory along with a single html file linking all the images. This is not recommended for a ChIP-Seq analysis such as this with >40k peaks since it (a) will take 9h to finish compared to minutes when run without generating reports and (b) will create a difficult to handle directory with >40k files.

Create a batch input file (e.g. peakranger.sh) for processing each experiment/control pair. For example:

#!/bin/bash

expt="${1:-none}"
ctrl="${2:-none}"
[[ "${expt}" == "none" || "${ctrl}" == "none" ]] && exit 1

module load peakranger/1.18 || exit 1
module load ucsc samtools || exit 1

peakranger nr --data "${expt}" --control "${ctrl}" --format bam > "${expt%bam}.noiserate"
peakranger wig --format bam --data "${expt}" --output "${expt%bam}wig"
samtools view -H ENCFF374UMR.bam | grep '^@SQ' | tr ':' '\t' | cut -f3,5 > chroms
wigToBigWig -clip "${expt%bam}wig" chroms "${expt%bam}bw"
peakranger ranger --data "${expt}" --control "${ctrl}" --format bam \
    --thread $SLURM_CPUS_PER_TASK --output ${expt%.bam}

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=8g peakranger.sh ENCFF374UMR.bam ENCFF700UBO.bam

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

peakranger nr --data expt1.bam --control control.bam --format bam > expt1.noiserate
peakranger nr --data expt2.bam --control control.bam --format bam > expt2.noiserate
peakranger nr --data expt3.bam --control control.bam --format bam > expt3.noiserate

Submit this job using the swarm command.

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