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* |
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
HOMER data
We maintain the HOMER data in a central location, which can be accessed and shared by all versions of HOMER. Current availabe data are listed below:
| Data | Packages |
|---|---|
| Organisms | human-o v6.0, rat-o v6.0, mouse-o v6.3 |
| Genomes | hg19 v6.0, rn5 v6.0, hg38 v6.0, nm10 v6.0 |
| Promoters | mouse-p v5.5 |
You can access the data via the environment variable $HOMER_DATA after loading the homer module. If you need other data, please contact OSC Help.
Usage on Owens
Set-up
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
$HOMER_DATA/genomes. To use proper genome database with annotatePeaks.pl tool, you need to specify the path to the genomes directory, e.g.annotatePeaks.pl input.bed $HOMER_DATA/genomes/mm10 > output.txt
#!/bin/bash
#SBATCH --job-name homer_data_test
#SBATCH --time=1:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --account=<project-account>
cp output_test.fastq $TMPDIR
module load homer/4.10
cd $TMPDIR
homerTools trim -3 GTCTTT -mis 1 -minMatchLength 4 -min 15 output_test.fastq
sgather -pr $TMPDIR ${SLURM_SUBMIT_DIR}/sgather
