---
name: "countsga"
section: "1"
platform: "linux"
package: "chip-seq"
version: "1.5.5-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/countsga"
---

# countsga(1)

read a ChIP-seq data file and computes the total number of tag counts

## NAME

countsga - read a ChIP-seq data file and computes the total number of tag counts

## SYNOPSIS

**countsga** \[*options*\] \[*\<*\] *\<SGA File\>*

## DESCRIPTION

-

  \- version 1.5.5 where options are:

- **-h**

  Show this help text

- **-d**

  Print debug information

- **-f**

  Feature specifications \[name \[+\|-\]\]

- **-c**

  Count Cut-off (default is 1)

-

  The program reads a ChIP-seq data file (or from stdin \[\<\]) in SGA format (\<SGA File\>), and computes the total number of tag counts as well as the total sequence length. The \<Feature\> parameter is a name that corresponds to the second field of the SGA file. It might optionally include the strand specification (+\|-). If no feature is given then all input tags are processed.

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.