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 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
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:
#!/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
Further Reading
Supercomputer:
Service:
Fields of Science: