---
name: "macs2"
section: "1"
platform: "linux"
package: "macs"
version: "2.2.7.1-6+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/macs2"
---

# macs2(1)

macs2 - Model-based Analysis for ChIP-Sequencing

## NAME

macs2 - macs2 - Model-based Analysis for ChIP-Sequencing

## DESCRIPTION

usage: macs2 \[-h\] \[--version\]

-

  {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak} ...

macs2 **--** Model-based Analysis for ChIP-Sequencing

### positional arguments:

-

  {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}

- callpeak

  Main MACS2 Function: Call peaks from alignment results.

- bdgpeakcall

  Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.

- bdgbroadcall

  Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.

- bdgcmp

  Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.

- bdgopt

  Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.

- cmbreps

  Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.

- bdgdiff

  Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.

- filterdup

  Remove duplicate reads at the same position, then save the rest alignments to BED or BEDPE file. If you use ' **--keep-dup** all option', this script can be utilized to convert any acceptable format into BED or BEDPE format.

- predictd

  Predict d or fragment size from alignment results. \*Will NOT filter duplicates\*

- pileup

  Pileup aligned reads with a given extension size (fragment size or d in MACS language). Note there will be no step for duplicate reads filtering or sequencing depth scaling, so you may need to do certain pre/postprocessing.

- randsample

  Randomly sample number/percentage of total reads.

- refinepeak

  (Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of waston/crick tags. Inspired by SPP.

### options:

- **-h**, **--help**

  show this help message and exit

- **--version**

  show program's version number and exit

For command line options of each command, type: macs2 COMMAND **-h**