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

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

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