HOMER

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.

Availability and Restrictions

Versions

The following versions of HOMER are available on OSC clusters:

Version owens
4.8 X*
4.10 X
* Current default version

You can use  module spider homer to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

HOMER is available to all OSC users without restriction.

Publisher/Vendor/Repository and License Type

Christopher Benner, Open source

Usage

Usage on Owens

Set-up

To configure your environment for use of HOMER, run the following command: module load homer. The default version will be loaded. To select a particular HOMER version, use module load homer/version. For example, use module load homer/4.10 to load HOMER 4.10.

Access HOMER Genome Data

Up-to-date HOMER genome data can be found in $HOMER_DATA/genomes. To the appropriate genome for analyzing genomic motifs, you can specify the path to a file or directory containing the genomic sequence in FASTA format and specify a path for preparsed data:
 
#PBS -N homer_data_test
#PBS -j oe 
#PBS -l walltime=1:00:00
#PBS -l nodes=1:ppn=1


cd $PBS_O_WORKDIR
cp peaks.txt $TMPDIR
mkdir -p $TMPDIR/preparsed

module load homer/4.10

cd $TMPDIR
findMotifsGenome.pl peaks.txt $HOMER_DATA/genomes/hg19 peakAnalysis -size 200 -preparsedDir $TMPDIR/preparsed

cp -a peakAnalysis $PBS_O_WORKDIR
 

Further Reading

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