---
name: "macs2_bdgpeakcall"
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_bdgpeakcall"
---

# macs2\_bdgpeakcall(1)

Model-based Analysis for ChIP-Sequencing

## NAME

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

## DESCRIPTION

usage: macs2 bdgpeakcall \[-h\] **-i** IFILE \[-c CUTOFF\] \[-l MINLEN\] \[-g MAXGAP\]

- \[--cutoff-analysis\] \[--no-trackline\]

  \[--outdir OUTDIR\] (**-o** OFILE \| **--o-prefix** OPREFIX)

### options:

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

  show this help message and exit

- **-i** IFILE, **--ifile** IFILE

  MACS score in bedGraph. REQUIRED

- **-c** CUTOFF, **--cutoff** CUTOFF

  Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. DEFAULT: 5

- **-l** MINLEN, **--min-length** MINLEN

  minimum length of peak, better to set it as d value. DEFAULT: 200

- **-g** MAXGAP, **--max-gap** MAXGAP

  maximum gap between significant points in a peak, better to set it as tag size. DEFAULT: 30

- **--cutoff-analysis**

  While set, bdgpeakcall will analyze number or total length of peaks that can be called by different cutoff then output a summary table to help user decide a better cutoff. Note, minlen and maxgap may affect the results. DEFAULT: False

- **--no-trackline**

  Tells MACS not to include trackline with bedGraph files. The trackline is required by UCSC.

- **--outdir** OUTDIR

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

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

  Output file name. Mutually exclusive with **--o-prefix**.

- **--o-prefix** OPREFIX

  Output file prefix. Mutually exclusive with **-o**/--ofile.