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

# chipcenter(1)

Feature Centering Tool for ChIP-seq data analysis

## NAME

chipcenter - Feature Centering Tool for ChIP-seq data analysis

## SYNOPSIS

**chipcenter \[** *options* **\]** **\[ -f** *\<feature name\>* **\]** **-s** *\<shift\>* **\[** *\<* **\]** **\[** *SGA file* **\]**

## DESCRIPTION

**chipcenter** reads a ChIP-seq data file (or from stdin \[\<\]) in SGA format (\<SGA file\>), and shifts (by \<shift\>) ChIP-tag positions corresponding to a specific feature (\<feature name\>) to the estimated center-positions of DNA fragments. If no feature specification is set, the program accepts all oriented lines of the input SGA. Strandless features are ignored. If -r \<new feature\> is specified, the feature field is replaced with the \<new feature\> string.

Launching **chipcenter** without any arguments will print the options list, along with their default values.

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.

## OPTIONS

- \-c \<cut-off\>

  A value can be specified as a cut-off for the input tag counts.

  This parameter is optional. Its default value is 1.

- \-d

  Show debug info.

- \-f \<feature name\>

  This parameter is used to select all or a sub-set of chIP-seq input tags. The feature name is specified in the second field of the SGA-formatted input file.

  If no feature name is given, then all features are selected.

- \-h

  Show the usage message.

- \-r \<new feature\>

  It defines a new feature name for feature replacement.

- \-s \<shift\>

  It defines the relative shift (in bp) of observed ChIP-tags to estimated center-positions of DNA fragments.

  This parameter is mandatory.

- \-z

  Set (output) strand to zero.

  This parameter is optional.

## SEE ALSO

[**chipcor**(1)](/chipcor/1.md), [**chipextract**(1)](/chipextract/1.md), [**chippeak**(1)](/chippeak/1.md) [**chippart**(1)](/chippart/1.md) [**chipscore**(1)](/chipscore/1.md),