JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets.

References:

• Ibrahim MM, Lacadie SA, Ohler U. JAMM: a peak finder for joint analysis of NGS replicates Bioinformatics. 2015 Jan 1;31(1):48-55.

• Main JAMM Site

• Module Name: JAMM (see the modules page for more information)
• Multithreaded
• Environment variables set
  • PATH
  • JAMM_EXAMPLES -- example files

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

[user@biowulf]$ sinteractive --cpus-per-task=16 --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 JAMM
[user@cn3144 ~]$ cp $JAMM_EXAMPLES/testdata.zip .
[user@cn3144 ~]$ unzip testdata.zip
[user@cn3144 ~]$ JAMM.sh -s testdata -g testdata/chrSizes21.csize -o JAMM.results -p $SLURM_CPUS_ON_NODE
[user@cn3144 ~]$
[user@cn3144 ~]$ JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files -g genome_size_file.txt -o /path/to/output -c /path/to/input/files

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

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

#!/bin/bash
module load JAMM
JAMM.sh \
  -p ${SLURM_CPUS_PER_TASK} \
  -s /path/to/sample/files \
  -g genome_size_file.txt \
  -o /path/to/output \
  -c /path/to/input/files

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=8g JAMM.sh

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

JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files1 \
  -g genome_size_file.txt -o /path/to/output1 -c /path/to/input/files1
JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files2 \
  -g genome_size_file.txt -o /path/to/output2 -c /path/to/input/files2
JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files3 \
  -g genome_size_file.txt -o /path/to/output3 -c /path/to/input/files3
JAMM.sh -p ${SLURM_CPUS_PER_TASK} -s /path/to/sample/files4 \
  -g genome_size_file.txt -o /path/to/output4 -c /path/to/input/files4

Submit this job using the swarm command.

swarm -f JAMM.swarm -g 8 -t 16 --module JAMM