---
name: "macs3_bdgdiff"
section: "1"
platform: "linux"
package: "macs"
version: "3.0.2-1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/macs3_bdgdiff"
---

# macs3\_bdgdiff(1)

Model-based Analysis for ChIP-Sequencing

## NAME

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

## DESCRIPTION

usage: macs3 bdgdiff \[-h\] **--t1** T1BDG **--t2** T2BDG **--c1** C1BDG **--c2** C2BDG

- \[-C CUTOFF\] \[-l MINLEN\] \[-g MAXGAP\] \[--d1 DEPTH1\]

  \[--d2 DEPTH2\] \[--verbose VERBOSE\] \[--outdir OUTDIR\] (**--o-prefix** OPREFIX \| **-o** OFILE OFILE OFILE)

### options:

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

  show this help message and exit

- **--t1** T1BDG

  MACS pileup bedGraph for condition 1. Incompatible with callpeak **--SPMR** output. REQUIRED

- **--t2** T2BDG

  MACS pileup bedGraph for condition 2. Incompatible with callpeak **--SPMR** output. REQUIRED

- **--c1** C1BDG

  MACS control lambda bedGraph for condition 1. Incompatible with callpeak **--SPMR** output. REQUIRED

- **--c2** C2BDG

  MACS control lambda bedGraph for condition 2. Incompatible with callpeak **--SPMR** output. REQUIRED

- **-C**, **--cutoff** CUTOFF

  log10LR cutoff. Regions with signals lower than cutoff will not be considerred as enriched regions. DEFAULT: 3 (likelihood ratio=1000)

- **-l**, **--min-len** MINLEN

  Minimum length of differential region. Try bigger value to remove small regions. DEFAULT: 200

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

  Maximum gap to merge nearby differential regions. Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length (**-g**). DEFAULT: 100

- **--d1**, **--depth1** DEPTH1

  Sequencing depth (# of non-redundant reads in million) for condition 1. It will be used together with **--d2**. See description for **--d2** below for how to assign them. Default: 1

- **--d2**, **--depth2** DEPTH2

  Sequencing depth (# of non-redundant reads in million) for condition 2. It will be used together with **--d1**. DEPTH1 and DEPTH2 will be used to calculate scaling factor for each sample, to down-scale larger sample to the level of smaller one. For example, while comparing 10 million condition 1 and 20 million condition 2, use **--d1** 10 **--d2** 20, then pileup value in bedGraph for condition 2 will be divided by 2. Default: 1

- **--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-prefix** OPREFIX

  Output file prefix. Actual files will be named as PREFIX\_cond1.bed, PREFIX\_cond2.bed and PREFIX\_common.bed. Mutually exclusive with **-o**/--ofile.

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

  Output filenames. Must give three arguments in order: 1. file for unique regions in condition 1; 2. file for unique regions in condition 2; 3. file for common regions in both conditions. Note: mutually exclusive with **--o-prefix**.