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JAMM

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:

There are multiple versions of JAMM available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail JAMM

To select a module, type

module load JAMM/[ver]

where [ver] is the version of choice.

Environment variables set:

JAMM is a multithreaded application. Make sure to match the number of cpus requested with the -p option.

On Helix

Sample session:

$ module load JAMM
$ JAMM.sh \
-p 4 \
-s /path/to/sample/files \
-g genome_size_file.txt \
-o /path/to/output \
-c /path/to/input/files
Batch job on Biowulf

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

#!/bin/bash
module load JAMM
JAMM.sh \
-p 16 \
-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-per-cpu=4g JAMM.sh
Swarm of Jobs on Biowulf

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

JAMM.sh -p 4 -s /path/to/sample/files1 -g genome_size_file.txt -o /path/to/output1 -c /path/to/input/files1
JAMM.sh -p 4 -s /path/to/sample/files2 -g genome_size_file.txt -o /path/to/output2 -c /path/to/input/files2
JAMM.sh -p 4 -s /path/to/sample/files3 -g genome_size_file.txt -o /path/to/output3 -c /path/to/input/files3
JAMM.sh -p 4 -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 4 -t 4 --module JAMM 
Interactive job on Biowulf
[biowulf]$ sinteractive --cpus-per-task=16 --mem-per-cpus=4g
[node]$ module load JAMM
[node]$ JAMM.sh -p 16 -s /path/to/sample/files -g genome_size_file.txt -o /path/to/output -c /path/to/input/files
Documentation