EDD is a ChIP-seq peak caller for detection of megabase domains of enrichment.

References:

• E Lund, AR Oldenburg, and P Collas Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations Nucl. Acids Res. 42 (2014)

• EDD on GitHub

• Module Name: edd (see the modules page for more information)
• Multithreaded
• Environment variables set:
  • EDD_EXAMPLES

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

[user@biowulf]$ sinteractive --cpus-per-task=8
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 edd
[user@cn3144 ~]$ ln -s $EDD_EXAMPLES/hg19.sizes .
[user@cn3144 ~]$ ln -s $EDD_EXAMPLES/*.bam .
[user@cn3144 ~]$ touch unalign.bed
[user@cn3144 ~]$ edd -p $SLURM_CPUS_PER_TASK -n 10000 hg19.sizes unalign.bed SRX447385.bam SRX447386.bam output_dir

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

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

#!/bin/bash

# Generate hg19 chrom sizes
module load ucsc
fetchChromSizes hg19 > hg19.sizes
module unload ucsc

# Create empty file for unalignable regions
touch unalign_empty

# Run the command, collecing output in output directory
ml edd
edd -p $SLURM_CPUS_PER_TASK -n 10000 hg19.sizes unalign.bed chip_seq.bam input.bam output_dir

Submit this job using the Slurm sbatch command.

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

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

edd -p $SLURM_CPUS_PER_TASK hg19.sizes unalign.bed chip_seq_1.bam input_1.bam output_dir_1
edd -p $SLURM_CPUS_PER_TASK hg19.sizes unalign.bed chip_seq_2.bam input_2.bam output_dir_2
edd -p $SLURM_CPUS_PER_TASK hg19.sizes unalign.bed chip_seq_3.bam input_3.bam output_dir_3
edd -p $SLURM_CPUS_PER_TASK hg19.sizes unalign.bed chip_seq_4.bam input_4.bam output_dir_4

Submit this job using the swarm command.

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