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. If you have any questions, please contact OSC Help.

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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