---
name: "bdgdiff"
section: "1"
platform: "linux"
package: "macs"
version: "2.0.9.1-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/bdgdiff"
---

# bdgdiff(1)

Naive call differential peaks from 4 bedGraph tracks for scores

## NAME

bdgdiff - Naive call differential peaks from 4 bedGraph tracks for scores

## SYNOPSIS

**bdgdiff** *\<--s1 bedGraph\> \<--s2 bedGraph\> \<--s12 bedGraph\> \<--s21 bedGraph\>* \[*-c CUTOFF*\] \[*-l MIN*\] \[*-g MAX*\] \[*-o PREFIX*\]

## DESCRIPTION

Call differential regions from four bedGraph files of pair-wise p/qvalue, with customized settings. Please read the descriptions of options carefully.

## OPTIONS

- **--version**

  show program's version number and exit

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

  Show this help message and exit.

- **--s1**=*ST1C1BDG*

  MACS p/qvalue score bedGraph, condition 1 ChIP treatment against condition 1 control input.

- **--s2**=*ST2C2BDG*

  MACS p/qvalue score bedGraph, condition 2 ChIP treatment against condition 2 control input.

- **--s12**=*ST1T2BDG*

  MACS p/qvalue score bedGraph, condition 1 ChIP treatment against condition 2 ChIP treatment.

- **--s21**=*ST2T1BDG*

  MACS p/qvalue score bedGraph, condition 2 ChIP treatment against condition 1 ChIP treatment.

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

  Cutoff depends on which method you used for score track. If the file contains p/qvalue scores from MACS2, score 5 means p/qvalue 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

- **-o** OPREFIX, **--o-prefix**=*OPREFIX*

  output file prefix, DEFAULT: peak