MACS3 — ChIP-seq and ATAC-seq Peak Caller

Overview

MACS3 (Model-based Analysis of ChIP-seq) identifies regions of significant read enrichment (peaks) from ChIP-seq, ATAC-seq, CUT&RUN, and CUT&TAG experiments. It models the fragment length distribution from paired-end data or estimates it from mono-nucleosomal read shifting in single-end data, then applies a Poisson model to identify fold-enrichment over an input/IgG control. MACS3 produces BED-format narrowPeak (for transcription factors) or broadPeak (for histone marks) files with signal and q-value tracks for visualization in IGV or UCSC Genome Browser.

When to Use

• Calling transcription factor binding peaks from ChIP-seq experiments (use --nomodel --extsize 200 or let MACS3 estimate fragment length)
• Identifying open chromatin regions from ATAC-seq experiments (use --nomodel --shift -100 --extsize 200 -f BAMPE)
• Calling broad histone modification peaks (H3K27me3, H3K9me3, H3K36me3) with --broad
• Generating peak signal tracks (bedGraph/bigWig) for genome browser visualization with -B --SPMR
• Performing differential binding analysis: MACS3 peaks as input to DiffBind or DESeq2
• Use HMMRATAC (part of MACS3) for nucleosome-resolution ATAC-seq peak calling
• Use SPP or HOMER as alternatives; MACS3 is the ENCODE-recommended standard

Prerequisites