Model Based Analysis for ChIP-Seq data
Project description
MACS: Model-based Analysis for ChIP-Seq
Latest Release:
Introduction
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, although 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. More new featuer will be added soon.
Recent Changes for MACS (3.0.0a1)
3.0.0a1
* Features
1) Speed/memory optimization, including using the cykhash to
replace python dictionary
2) Code cleanup
3) Unit testing
4) R wrappers for MACS
5) Switching to Github Action for CI, support multi-arch testing.
Install
The common way to install MACS is through PYPI) or conda. Please check the INSTALL document for detail.
Usage
Example for regular peak calling on TF ChIP-seq:
macs2 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:
macs2 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1
Example for peak calling on ATAC-seq (paired-end mode):
macs2 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.
Subcommand | Description |
---|---|
callpeak |
Main MACS3 Function to call peaks from alignment results. |
bdgpeakcall |
Call peaks from bedGraph output. |
bdgbroadcall |
Call broad peaks from bedGraph output. |
bdgcmp |
Comparing two signal tracks in bedGraph format. |
bdgopt |
Operate the score column of bedGraph file. |
cmbreps |
Combine BEDGraphs of scores from replicates. |
bdgdiff |
Differential peak detection based on paired four bedGraph files. |
filterdup |
Remove duplicate reads, then save in BED/BEDPE format. |
predictd |
Predict d or fragment size from alignment results. |
pileup |
Pileup aligned reads (single-end) or fragments (paired-end) |
randsample |
Randomly choose a number/percentage of total reads. |
refinepeak |
Take raw reads alignment, refine peak summits. |
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.
Contribute
Please read our CODE OF CONDUCT and How to contribute documents.
Ackowledgement
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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