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. 2012 Sep;7(9):1728-40.
doi: 10.1038/nprot.2012.101. Epub 2012 Aug 30.

Identifying ChIP-seq enrichment using MACS

Jianxing Feng  1 , Tao Liu, Bo Qin, Yong Zhang, Xiaole Shirley Liu
Affiliations

Identifying ChIP-seq enrichment using MACS

Jianxing Feng et al. Nat Protoc. 2012 Sep.

Abstract

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/.

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Figures

Figure 1
Figure 1
Workflow of MACS 1.4.2. If the control sample is missing, then the steps shown in white boxes will be skipped (Remove redundancy of the control sample, Scale two libraries, and Calculate FDR by exchanging treatment and control).
Figure 2
Figure 2
Peak model built by MACS using the FoxA1 dataset. d=114 represents the estimated DNA fragment size. The red curve represents the percentage of positive strand reads at each base pair, and the blue curve models reads on the negative strand. The black curve illustrates the distribution of reads after shifting them towards the 3’ end by 57=114/2 bp.
Figure 3
Figure 3
IGV visualization of MACS results using the FoxA1 dataset. This region is selected from chromosome 1, as shown at the top of the figure. The middle section of the figure illustrates the pileup signal after extending all reads to the estimated fragment size in the top track (labeled FoxA1_treat_chr1). Below this, the middle track, labeled FoxA1_peaks.bed, shows two peaks identified by MACS. The bottom track, labeled FoxA1_peaks.subpeaks.bed, shows three sub-peaks generated by PeakSplitter. The bottom track, labeled hg19refGene, shows the gene annotation of the human genome assembly of version hg19.
Figure 4
Figure 4
IGV visualization of MACS results using the University of Washington H3K4me3 dataset. The region on chromosome 1 (shown in the top section of the figure) shows three peaks are identified by MACS in the middle section. These three peaks are located in the promoter regions of three genes, shown in the bottom part of the figure.
Figure 5
Figure 5
IGV visualization of MACS results using the Broad Institute H3K36me3 dataset. The selected region spans the whole gene body of SMURF1 shown in the bottom part of the figure. The middle section of the figures shows that H3K36me3 signal is more enriched in exon regions, as demonstrated in the second track (H3K36me3_treat_chr7). MACS identifies such enriched regions as multiple peaks, shown in the third track (H3K36me3_peaks.bed).
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