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With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we presented the Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with a control sample with the increase of specificity. Moreover, as a general peak-caller, MACS can also be applied to any "DNA enrichment assays" if the question to be asked is simply: where we can find significant reads coverage than the random background.

Please note that current MACS3 is still in beta stage. However, we utilize Github Action to implement the CI (Continous Integration) to make sure that the main branch passes unit testing on certain functions and subcommands to reproduce the correct outputs. We will add more new features in the future.

The second beta version of MACS3, with HMMRATAC feature refined.
   
* New features from beta1:

1) HMMRATAC module fixes

   Cutoff analysis function added
   Description regarding it has been added

2) Memory monitoring in the runtime message

3) testing for s390x, armv7 and power64le is back. However, we turned off the function to check if the `hmmratac` results from non-x86 architectures are the same as the standard results, because in order to let the testing run, we need to use old python libraries (scipy and sklearn) through the distribution of Debian/Linux bullseye.

The common way to install MACS is through PYPI) or conda. Please check the INSTALL document for detail.

MACS3 has been tested in CI for every push and PR in the following architectures:

• x86_64
• aarch64
• armv7
• ppc64le
• s390x

Example for regular peak calling on TF ChIP-seq:

macs3 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01

Example for broad peak calling on Histone Mark ChIP-seq:

macs3 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1

Example for peak calling on ATAC-seq (paired-end mode):

macs3 callpeak -f BAMPE -t ATAC.bam -g hs -n test -B -q 0.01

There are currently 14 functions available in MACS3 serving as sub-commands. Please click on the link to see the detail description of the subcommands.

For advanced usage, for example, to run macs3 in a modular way, please read the advanced usage. There is a Q&A document where we collected some common questions from users.

Please read our CODE OF CONDUCT and How to contribute documents. If you have any questions, suggestion/ideas, or just want to have conversions with developers and other users in the community, we recommand you use the MACS Discussions instead of posting to our Issues page.

MACS3 project is sponsored by CZI EOSS. And we particularly want to thank the user community for their supports, feedbacks and contributions over the years.

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