Introduction

MOTIVATION: Post-translational modifications to histones have several well known associations with regulation of gene expression. While some modifications appear concentrated narrowly, covering promoters or enhancers, others are dispersed as epigenomic domains. These domains mark contiguous regions sharing an epigenomic property, such as actively transcribed or poised genes, or heterochromatically silenced regions. While high-throughput methods like ChIP-Seq have led to a flood of high-quality data about these epigenomic domains, there remain important analysis problems that are not adequately solved by current analysis tools. RESULTS: We present the RSEG method for identifying epigenomic domains from ChIP-Seq data for histone modifications. In contrast with other methods emphasizing the locations of 'peaks' in read density profiles, our method identifies the boundaries of domains. RSEG is also able to incorporate a control sample and find genomic regions with differential histone modifications between two samples. AVAILABILITY: RSEG, including source code and documentation, is freely available at http://smithlab.cmb.usc.edu/histone/rseg/.

Publications

  1. Identifying dispersed epigenomic domains from ChIP-Seq data.
    Cite this
    Song Q, Smith AD, 2011-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Qiang Song
    Developer

  2. Andrew D Smith
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT007008
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAndrew D Smith