---
name: "macs3_cmbreps"
section: "1"
platform: "linux"
package: "macs"
version: "3.0.2-1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/macs3_cmbreps"
---

# macs3\_cmbreps(1)

Model-based Analysis for ChIP-Sequencing

## NAME

mac3\_cmbreps - Model-based Analysis for ChIP-Sequencing

## DESCRIPTION

usage: macs3 cmbreps \[-h\] **-i** IFILE \[IFILE ...\] \[-m {fisher,max,mean}\]

-

  \[--outdir OUTDIR\] **-o** OFILE \[--verbose VERBOSE\]

### options:

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

  show this help message and exit

- **-i** IFILE \[IFILE ...\]

  MACS score in bedGraph for each replicate. Require at least 2 files such as '-i A B C D'. REQUIRED

- **-m**, **--method** {fisher,max,mean}

  Method to use while combining scores from replicates. 1) fisher: Fisher's combined probability test. It requires scores in ppois form (**-log10** pvalues) from bdgcmp. Other types of scores for this method may cause cmbreps unexpected errors. 2) max: take the maximum value from replicates for each genomic position. 3) mean: take the average value. Note, except for Fisher's method, max or mean will take scores AS IS which means they won't convert scores from log scale to linear scale or vice versa.

- **--outdir** OUTDIR

  If specified all output files will be written to that directory. Default: the current working directory

- **-o**, **--ofile** OFILE

  Output BEDGraph filename for combined scores.

- **--verbose** VERBOSE

  Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2