Introduction

ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs. control, and identify regions that show differences in ChIP enrichment. We have developed a powerful and easy to use program, called diffReps, to detect those differential sites from ChIP-seq data, with or without biological replicates. In addition, we have developed two useful tools for ChIP-seq analysis in the diffReps package: one for the annotation of the differential sites and the other for finding chromatin modification "hotspots". diffReps is developed in PERL programming language and runs on all platforms as a command line script. We tested diffReps on two different datasets. One is the comparison of H3K4me3 between two human cell lines from the ENCODE project. The other is the comparison of H3K9me3 in a discrete region of mouse brain between cocaine- and saline-treated conditions. The results indicated that diffReps is a highly sensitive program in detecting differential sites from ChIP-seq data.

Publications

  1. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.
    Cite this
    Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ, 2013-01-01 - PloS one

Credits

  1. Li Shen
    Developer

    Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai

  2. Ning-Yi Shao
    Developer

  3. Xiaochuan Liu
    Developer

  4. Ian Maze
    Developer

  5. Jian Feng
    Developer

  6. Eric J Nestler
    Investigator

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Summary
AccessionBT000223
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByEric J Nestler