MACS pipeline

MACS specifications


Unique identifier OMICS_00446
Alternative names Model-based Analysis for ChIP-Seq, MACS2, macs2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A tag file, a treatment file.
Output data A file with information about called peaks, peak locations, peak summits locations, negative peaks, a script to produce a PDF image, a file that can be viewed through the UCSC genome browser, a diagnosis report and an optional file for the subpeaks option.
Output format XLS+BED+R+bedGraph+XLS+TXT
Operating system Unix/Linux
Programming languages C, Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 2.1.0
Stability Stable
Requirements Numpy, GCC, Cython
Maintained Yes


  • MACS2-bdgdiff



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  • person_outline Wei Li <>
  • person_outline Tao Liu <>

Additional information

Publication for Model-based Analysis for ChIP-Seq

MACS citations

PMCID: 5918530

[…] hg38 reference genome using bowtie2 (version 2.3.1) (langmead and salzberg, 2012) using default parameters except that up to one mismatch was accepted in the seed sequence. peaks were identified by macs2 (version 2.1.1) (zhang et al., 2008) using the input sample as a control while bypassing the shifting model and with the broad peak setting with a broad cutoff of 0.05 for h3k4me3 and h3k79me2 […]

PMCID: 5626401

[…] (hg19) human reference sequence using bwa-mem (li and durbin, 2009). after alignment, technical replicates were merged and all further analyses were performed on these merged data. for peak calling, macs2 (zhang et al., 2008) was used with no-model, 100-bp shift, 200-bp extension, and broad peaks options. only peaks called with a peak score (q-value) of 1% or better were kept from each sample, […]

PMCID: 5570084

[…] default parameters. the reads were mapped to the reference genome using bowtie v2 2.1.0. the non-unique reads were randomly distributed. binding enrichment was called from the aligned reads using macs2 2.0.10 and spp ( using default parameters. all statistical analyses were performed using r., the 5΄ end hypermethylated spliced leader (sl) […]

PMCID: 5442315

[…] respectively, for peak-calling from the same sequencing depth in all samples65. significant enrichment regions in h3k4me3 and h3k27me3 samples, relative to h3 control samples, were identified using macs2 2.1.0 (default settings for h3k4me3—fdr<0.05; broad-peaks mode for h3k27me3—fdr<0.1)6667. regions with signal level measured by fpkm(chip)/fpkm(h3 control) differing between biological […]

PMCID: 5259890

[…] reads were subsequently filtered for alignment quality of > q30 and were required to be properly paired. reads mapping to the mitochondria or chromosome y were removed and not considered. we used macs2 ( to call all reported atac-seq peaks. macs2 was used with the following parameters (--nomodel --shift 0). peaks were filtered using the consensus excludable […]

MACS institution(s)
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA; Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Gene Security Network, Inc., Redwood City, CA, USA; Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital and Department of Pathology, Harvard Medical School, Charlestown, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Genetics, Stanford University Medical Center, Stanford, CA, USA; Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
MACS funding source(s)
Supported in part by NIH grants HG004069, HG004270 and DK074967.

MACS reviews

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Miklós Laczik

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Arguably a gold standard among peak callers, MACS is excellent in detecting significant enrichments in point-source enrichment type NGS data, like ChIP-seq data with transcription factors. It is easy to use, well documented, well maintained. It can be run both with or without a control sample, and the options give you a decent flexibility (setting significance treshold, switching the model building on or off, determining the fragment size to match the experimentally determined size, working with various file formats from BED through BAM to proprietary Illumina formats etc.) It has a decent speed too.
I think it's important to understand that it is designed for point-source data, and for that it works perfectly (that's why I gave maximum rating, despite the constraints described in the following section, which I don't see as a fault - it's really not intended for the tasks below.) Numerous tests show (even a paper published by the MACS authors) that when it comes to diffuse enrichments, most notably, ChIP-seq with histone marks, then MACS fails to identify the peaks correctly. Usually it manages to detect some parts of it, some local summits within the dispersed signal, if it detects something at all. Although in the literature it is used for various datasets, including histone marks, ATAC-seq, MeDIP-seq etc., I wouldn't recommend it for detecting other enrichments than point-source peaks. There are much superior tools out there for diffuse signals (like SICER). I have to mention though that maybe H3K4me3 is an exception, it is a very "TF-like" histone mark, with sharp, clear, high enrichments, and for that mark only MACS might be acceptable. But I wouldn't trust it for any other HMs (and I've been working with ChIP-seq data of all histone marks you can imagine for ~10 years). I would also take the results of MeDIP-seq. ATAC-seq and similar data with a grain of salt if it was processed with MACS, because while it can certainly detect some enrichment, not all ofthem can be considered point-source, many methylated regions, open chromatin etc. are way broader than that.

With that said, I think it's a great tool for what it was designed.
Be aware that the MACS website is still saying that the newest version is version 1.4.2, which is not true, it has long been superceded by the major version 2, which you can find on GitHub (at the time of writing this review the latest stable version is 2.1.0).

Fabien Pichon

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A very good software to find peaks in ChIP-seq experiments (except for broad peaks like H3K27me3 and H3K36me3 where you should prefer SICER). Also works perfectly with ATAC-seq where you can use it without input (-c option).
Easy to install and use.