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HOMER (v4.7, 8-25-2014)

Software for motif discovery and next generation sequencing analysis

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.

News

(8-25-2014) Many upgrades and bug-fixes.  Fixed issues with strand specific read counting and sizing issues with annotatePeaks.pl.  Updates to accession numbers and GTF parsing too.

(3-29-2014) New version v4.6. Better super enhancer code, plus lots of other minor upgrades.

(1-27-2014) New version v4.5 with updated genome packages too - Last version did not correctly assign priority assignments in annotations (i.e. TSS > exons > introns > intergenic was not honored in last version - fixed now).  Problems with some of the update scripts too.  Website updates are ongoing.

(1-23-2014) Updated All Organism Packages to v1.1 - latest packages lacked the org2gene.tsv file (i.e. human2gene.tsv).  Users that updated from the older version of HOMER probably didn't notice since the old files would have still been there - new users probably got an error.

(1-15-2014) Welcome to homer.salk.edu - new host for HOMER!

(1-15-2014) Lots of new documentation.  More new documentation will probably be added to the site over the next week or so, and new PDF's will be created once that gets in good shape.

(1-14-2014) New version v4.4. New version with changes to configuration to help separate the code and data, update scripts to keep annotation/accessions up-to-date and incorporate custom genomes/organisms.  As always, lots of new features and bug fixes.  It's very likely a new version will be posted soon to smooth out any details.  Major changes to note:
  1. Major Updates to annotations and custom configuration - easier to add your own genome or annotation
  2. bedGraphs and coverage histrograms are now normalized for fragment length (this is a GOOD upgrade, be careful comparing to old results)

Old News

Program Download

Download Page - Get the latest version of HOMER

Supported Organisms: Human (hg17, hg18, hg19), Mouse (mm8, mm9, mm10), Rat (rn4, rn5), Frog (xenTro2, xenTro3), Zebrafish (danRer7), Drosophila (dm3), C elegans (ce6, ce10), S. cerevisiae (sacCer2, sacCer3), pombe (ASM294v1), Arabidopsis (tair10), Rice (msu6), and also works with custom genomes in FASTA format and gene annotations in GTF format.

Using HOMER

Introduction to HOMER

Duff-sponsored Tutorials

General Introduction to Next-Gen Sequencing Analysis Tutorial
Useful for those new to sequencing
HOMER Next-gen Sequencing Tutorial [PDF-old]

Helps guide and explain how to use HOMER for ChIP-Seq/GRO-Seq/MNase-Seq/DNase-Seq/RNA-Seq etc. analysis

Old tutorial: Analysis of ChIP-Seq experiments using HOMER (some of this is out-of-date)

HOMER Motif Finding Tutorial [PDF-old]

Instructions and advice for finding enriched regulatory elements from a set of genome positions, a list of genes, or raw FASTA files.
HOMER Hi-C Analysis Tutorial [PDF-old]
Description of routines for analysis of Hi-C data to study genome conformation and structure.
Doughnut Documentation

Primary Data Download

HOMER Known Motifs - Genome-wide predictions and UCSC Track

These tracks display motif positions genome-wide for human and mouse.  They are based on HOMER-motifs, and certainly miss many "weak" binding sites and incorrectly predict others.  However, the preictions can still serve as a useful guide to where factors are likely to bind (if they're expressed in the system you're studying).

Mouse mm9 UCSC BigBed Track (load as a custom track) - [primary BED file]
Human hg19 UCSC BigBed Track (load as a custom track) - [primary BED file]

Data included in HOMER that may be useful for other purposes


UCSC Visualization files (Updated for errors in UCSC processing 08/31/10)

ChIP-Seq from the Glass, Murre, and Katzenellenbogen Labs

Credits

HOMER was developed primarily by Chris Benner, with significant contributions and suggestions by Sven Heinz, Kasey Hutt, Yin Lin, Gene Hsiao, Fernando Alcalde, Josh Stender, Amy Sullivan, Nathan Spann, Ivan Garcia-Bassets, Michael Lam, Michael Rehli, and many others.  Initial supervision for the project was provided by Professors Christopher K. Glass and Shankar Subramaniam.

Development of HOMER is carried out in the Integrative Genomics and Bioinformatics Core at the Salk Institute.  HOMER was initially developed in the Glass Lab at UCSD.

For now, if you use HOMER in your research, please cite the following paper:
Heinz S, Benner C, Spann N, Bertolino E et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell 2010 May 28;38(4):576-589. PMID: 20513432

Link to the raw data: GSE21512
Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@salk.edu