---
name: "macs3_bdgbroadcall"
section: "1"
platform: "linux"
package: "macs"
version: "3.0.2-1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/macs3_bdgbroadcall"
---

# macs3\_bdgbroadcall(1)

Model-based Analysis for ChIP-Sequencing

## NAME

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

## DESCRIPTION

usage: macs3 bdgbroadcall \[-h\] **-i** IFILE \[-c CUTOFFPEAK\] \[-C CUTOFFLINK\]

- \[-l MINLEN\] \[-g LVL1MAXGAP\] \[-G LVL2MAXGAP\]

  \[--no-trackline\] \[--verbose VERBOSE\] \[--outdir OUTDIR\] (**-o** OFILE \| **--o-prefix** OPREFIX)

### options:

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

  show this help message and exit

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

  MACS score in bedGraph. REQUIRED

- **-c**, **--cutoff-peak** CUTOFFPEAK

  Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS3, score 2 means qvalue 0.01. Regions with signals lower than cutoff will not be considerred as enriched regions. DEFAULT: 2

- **-C**, **--cutoff-link** CUTOFFLINK

  Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS3, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1

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

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

- **-g**, **--lvl1-max-gap** LVL1MAXGAP

  maximum gap between significant peaks, better to set it as tag size. DEFAULT: 30

- **-G**, **--lvl2-max-gap** LVL2MAXGAP

  maximum linking between significant peaks, better to set it as 4 times of d value. DEFAULT: 800

- **--no-trackline**

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

- **--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

- **--outdir** OUTDIR

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

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

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

- **--o-prefix** OPREFIX

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