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
The following versions of HOMER are available on OSC clusters:
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.
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 on Owens
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/4.10to load HOMER 4.10.
Access HOMER Genome Data
$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