chipcenter1
Feature centering tool for chip-seq data analysis
Usage
chipcenter [options]
[-f
<feature
name>]
-s
<shift>
[<]
[SGA
file]
Overview
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.
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).