MACS: Model-based Analysis for ChIP-Seq
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 alpha 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.
Recent Changes for MACS (3.0.0a6)
* New features 1) Speed/memory optimization. Use the cykhash to replace python dictionary. Use buffer (10MB) to read and parse input file (not available for BAM file parser). And many optimization tweaks. 2) Code cleanup. Reorganize source codes. 3) Unit testing. 4) R wrappers for MACS -- MACSr matching the current version of MACS 5) Switch to Github Action for CI, support multi-arch testing including x64, armv7, aarch64, s390x and ppc64le. 6) MACS tag-shifting model has been refined. Now it will use a naive peak calling approach to find ALL possible paired peaks at + and - strand, then use all of them to calculate the cross-correlation. (a related bug has been fix #442) 7) Call variants in peak regions directly from BAM files. The function was originally developed under code name SAPPER. Now SAPPER has been merged into MACS. Also, `simde` has been added as a submodule in order to support fermi-lite library under non-x64 architectures.
MACS3 has been tested in CI for every push and PR in the following architectures:
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 twelve functions available in MAC3 serving as sub-commands. Please click on the link to see the detail description of the subcommands.
||Main MACS3 Function to call peaks from alignment results.|
||Call peaks from bedGraph output.|
||Call broad peaks from bedGraph output.|
||Comparing two signal tracks in bedGraph format.|
||Operate the score column of bedGraph file.|
||Combine BEDGraphs of scores from replicates.|
||Differential peak detection based on paired four bedGraph files.|
||Remove duplicate reads, then save in BED/BEDPE format.|
||Predict d or fragment size from alignment results.|
||Pileup aligned reads (single-end) or fragments (paired-end)|
||Randomly choose a number/percentage of total reads.|
||Take raw reads alignment, refine peak summits.|
||Call variants in given peak regions from the alignment BAM files.|
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.