---
name: "macs3"
section: "1"
platform: "linux"
package: "macs"
version: "3.0.2-1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/macs3"
---

# macs3(1)

macs3 - Model-based Analysis for ChIP-Sequencing

## NAME

macs3 - macs3 - Model-based Analysis for ChIP-Sequencing

## DESCRIPTION

usage: macs3 \[-h\] \[--version\]

-

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

macs3 **--** Model-based Analysis for ChIP-Sequencing

### positional arguments:

-

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

- callpeak

  Main MACS3 Function: Call peaks from alignment results.

- bdgpeakcall

  Call peaks from bedGraph file.

- bdgbroadcall

  Call nested broad peaks from bedGraph file.

- bdgcmp

  Comparing two signal tracks in bedGraph format.

- bdgopt

  Operate the score column of bedGraph file.

- cmbreps

  Combine bedGraph files of scores from replicates.

- bdgdiff

  Differential peak detection based on paired four bedGraph files.

- filterdup

  Remove duplicate reads, then save in BED/BEDPE format file.

- predictd

  Predict d or fragment size from alignment results. In case of PE data, report the average insertion/fragment size from all pairs.

- pileup

  Pileup aligned reads (single-end) or fragments (paired-end).

- randsample

  Randomly choose a number/percentage of total reads, then save in BED/BEDPE format file.

- refinepeak

  Take raw reads alignment, refine peak summits. Inspired by SPP.

- callvar

  Call variants in given peak regions from the alignment BAM files.

- hmmratac

  Dedicated peak calling based on Hidden Markov Model for ATAC-seq data.

### 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: macs3 COMMAND **-h**