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HOMER on Biowulf

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 program to create peak files from BED files).

The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.

$ module avail homer
---------------------- /usr/local/Modules/3.2.9/modulefiles --------------------------------
homer/3.10         homer/3.11         homer/3.13         homer/3.15         homer/4.0(default)

$ module load homer

$ module list
Currently Loaded Modulefiles:
1) homer/4.0 $ module unload homer $ module load homer/3.11 $ module list Currently Loaded Modulefiles: 1) homer/3.11 $ module show homer ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/homer/4.0: module-whatis Sets up homer 4.0 prepend-path PATH /usr/local/apps/homer/4.0/bin -------------------------------------------------------------------


Prebuilt Homer data can be found in /usr/local/apps/homer/data. If you don't see what you need, please contact us at


Sample Sessions On Biowulf

Submitting a single homer batch job

1. Create a script file alone the following lines.

# This file is runHomer
#PBS -m be
#PBS -k oe
module load homer
cd /data/$USER/homer1 genelist.txt mouse motifResults/ -len 10

3. Submit the script using the 'qsub' command on Biowulf.

qsub -l nodes=1:g8 /data/$USER/runHomer

Submitting a swarm of jobs

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile). Here is a sample file: genelist1.txt mouse motifResults1/ -len 10 genelist2.txt mouse motifResults2/ -len 10 genelist3.txt mouse motifResults3/ -len 10

By default, each line of the command file above will be executed on 1 processor core of a node and use 1gb of memory. If this is not what you want, you will need to specify '-g' flags when you submit the job on biowulf.

Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:

biowulf> $ swarm -g 10 --module homer -f cmdfile

For more information regarding running swarm, see swarm.html