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

# filter\_counts(1)

read a ChIP-seq data file and filters out all read counts

## NAME

filter\_counts - read a ChIP-seq data file and filters out all read counts

## SYNOPSIS

**filter\_counts** \[*options*\] \[*\<*\] *\<SGA File\>*

## DESCRIPTION

-

  \- version 1.5.5 where options are:

- **-h**

  Show this help text

- **-d**

  Print debug information

- **-f**

  Feature defining the user-defined regions of interest (default=RMSK)

- **-r**

  Retain Mode on

-

  The program reads a ChIP-seq data file (or from stdin \[\<\]) in SGA format (\<SGA File\>) and filters out all read counts that occur within user-defined regions of interest, such as Repeat Mask regions (feature=RMSK). If 'Retain Mode' is on, it only retains those lines that are within the user-defined regions, in which case the annotation of the user-defined regions is added to the output SGA file.

## AUTHOR

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