HOMER 4.10.3

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.

Accessing the software

To load the module:

$ module load HOMER/4.10.3-iomkl-2018a-Perl-5.26.1

An example command to include in your job script:

perl ${EBROOTHOMER}/bin/findMotifs.pl genelist.txt mouse motifResults/ -len 10

#This runs the findMotifs script with the input list genlist.txt using the mouse promoter set sending output to the directory motifResults with the additional option -len 10.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the HOMER website for more information regarding this application.

Last modified: 16 January 2019