.TH chipcenter 1 "July 2015" Bioinformatics "User Manuals"
.SH NAME
chipcenter \- Feature Centering Tool for ChIP-seq data analysis
.SH SYNOPSIS
.B chipcenter [
.I options
.B ]
.B [ -f
.I <feature name>
.B ]
.B -s
.I <shift>
.B [
.I <
.B ]
.B [
.I SGA file
.B ]
.SH DESCRIPTION
.B 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
.B 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.

.SH OPTIONS
.IP "-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.
.IP "-d"
Show debug info.
.IP "-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.
.IP "-h"
Show the usage message.

.IP "-r <new feature>"
It defines a new feature name for feature replacement.

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

This parameter is mandatory.
.IP "-z "
Set (output) strand to zero.

This parameter is optional.
.SH "SEE ALSO"
.BR chipcor (1),
.BR chipextract (1),
.BR chippeak (1)
.BR chippart (1)
.BR chipscore (1),