Introduction

Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) can identify genomic regions that bind proteins involved in various chromosomal functions. Although the development of next-generation sequencers offers the technology needed to identify these protein-binding sites, the analysis can be computationally challenging because sequencing data sometimes consist of >100 million reads/sample. Herein, we describe a cost-effective and time-efficient protocol that is generally applicable to ChIP-seq analysis; this protocol uses a novel peak-calling program termed DROMPA to identify peaks and an additional program, parse2wig, to preprocess read-map files. This two-step procedure drastically reduces computational time and memory requirements compared with other programs. DROMPA enables the identification of protein localization sites in repetitive sequences and efficiently identifies both broad and sharp protein localization peaks. Specifically, DROMPA outputs a protein-binding profile map in pdf or png format, which can be easily manipulated by users who have a limited background in bioinformatics.

Publications

  1. DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.
    Cite this
    Nakato R, Itoh T, Shirahige K, 2013-07-01 - Genes to cells : devoted to molecular & cellular mechanisms

Credits

  1. Ryuichiro Nakato
    Developer

    Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, Japan

  2. Tahehiko Itoh
    Developer

  3. Katsuhiko Shirahige
    Investigator

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Summary
AccessionBT006956
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByKatsuhiko Shirahige