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Homer on Biowulf & Helix

HOMER offers solid tools and methods for interpreting ChIP-Seq experiments. In addition to UCSC visualization support and peak finding [and motif finding of course], HOMER can help assemble data across multiple experiments and look at positional specific relationships between sequencing tags, motifs, and other features. You do not need to use the peak finding methods in this package to use motif finding. (Use the bed2pos.pl program to create peak files from BED files).

Prebuilt data files are located in /fdb/homer

Running on Helix

$ module load homer
$ cd /data/$USER/Examples
$ findMotifs.pl genelist.txt mouse Results -len 10

Running a single batch job on Biowulf

1. Create a script file similar to the lines below.

#!/bin/bash

module load homer
cd /data/$USER/Examples
findMotifs.pl genelist.txt mouse Results -len 10

2. Submit the script on biowulf:

$ sbatch jobscript

For more memory requirement (default 4gb), use --mem flag:

$ sbatch --mem=10g jobscript

Running a swarm of jobs on Biowulf

Setup a swarm command file:

  cd /data/$USER/dir1; findMotifs.pl genelist.txt mouse Results -len 10
  cd /data/$USER/dir2; findMotifs.pl genelist.txt mouse Results -len 10
  cd /data/$USER/dir3; findMotifs.pl genelist.txt mouse Results -len 10
	[......]  

Submit the swarm file:

  $ swarm -f swarmfile --module homer

-f: specify the swarmfile name
--module: set environmental variables for each command line in the file

To allocate more memory, use -g flag:

  $ swarm -f swarmfile -g 10 --module homer

-g: allocate more memory

For more information regarding running swarm, see swarm.html

Running an interactive job on Biowulf

It may be useful for debugging purposes to run jobs interactively. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

biowulf$ sinteractive 
salloc.exe: Granted job allocation 16535

cn999$ module load homer
cn999$ cd /data/$USER/Examples
cn999$ findMotifs.pl genelist.txt mouse Results -len 10
[...etc...]

cn999$ exit
exit

biowulf$

Make sure to exit the job once finished.

If more memory is needed, use --mem flag. For example

biowulf$ sinteractive --mem=10g

Documentation

http://homer.salk.edu/homer/