Document Detail


Identifying ChIP-seq enrichment using MACS.
MedLine Citation:
PMID:  22936215     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Model-based analysis of ChIP-seq (MACS) is a computational algorithm that identifies genome-wide locations of transcription/chromatin factor binding or histone modification from ChIP-seq data. MACS consists of four steps: removing redundant reads, adjusting read position, calculating peak enrichment and estimating the empirical false discovery rate (FDR). In this protocol, we provide a detailed demonstration of how to install MACS and how to use it to analyze three common types of ChIP-seq data sets with different characteristics: the sequence-specific transcription factor FoxA1, the histone modification mark H3K4me3 with sharp enrichment and the H3K36me3 mark with broad enrichment. We also explain how to interpret and visualize the results of MACS analyses. The algorithm requires ∼3 GB of RAM and 1.5 h of computing time to analyze a ChIP-seq data set containing 30 million reads, an estimate that increases with sequence coverage. MACS is open source and is available from http://liulab.dfci.harvard.edu/MACS/.
Authors:
Jianxing Feng; Tao Liu; Bo Qin; Yong Zhang; Xiaole Shirley Liu
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2012-08-30
Journal Detail:
Title:  Nature protocols     Volume:  7     ISSN:  1750-2799     ISO Abbreviation:  Nat Protoc     Publication Date:  2012 Sep 
Date Detail:
Created Date:  2012-08-31     Completed Date:  2012-12-10     Revised Date:  2014-01-10    
Medline Journal Info:
Nlm Unique ID:  101284307     Medline TA:  Nat Protoc     Country:  England    
Other Details:
Languages:  eng     Pagination:  1728-40     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Chromatin Immunoprecipitation / methods*
Hepatocyte Nuclear Factor 3-alpha / genetics*
High-Throughput Nucleotide Sequencing / methods*
Histones / genetics*
Models, Genetic*
Software*
Grant Support
ID/Acronym/Agency:
HG4069/HG/NHGRI NIH HHS; R01 HG004069/HG/NHGRI NIH HHS
Chemical
Reg. No./Substance:
0/FOXA1 protein, human; 0/Hepatocyte Nuclear Factor 3-alpha; 0/Histones
Comments/Corrections

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