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Curr Protoc Bioinformatics. 2011 Jun;Chapter 2:Unit 2.14. doi: 10.1002/0471250953.bi0214s34.

Using MACS to identify peaks from ChIP-Seq data.

Author information

1
School of Life Sciences and Technology, Tongji University, Shanghai, China.

Abstract

Model-based Analysis of ChIP-Seq (MACS) is a command-line tool designed by X. Shirley Liu and colleagues to analyze data generated by ChIP-Seq experiments in eukaryotes, especially mammals. MACS can be used to identify transcription factor binding sites and histone modification-enriched regions if the ChIP-Seq data, with or without control samples, are given. This unit describes two basic protocols that provide detailed information on how to use MACS to identify either the binding sites of a transcription factor or the enriched regions of a histone modification with broad peaks. Furthermore, the basic ideas for the MACS algorithm and its appropriate usage are discussed.

PMID:
21633945
PMCID:
PMC3120977
DOI:
10.1002/0471250953.bi0214s34
[Indexed for MEDLINE]
Free PMC Article

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