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), chipextract(1), chippeak(1) chippart(1) chipscore(1),

Bioinformatics                                      July 2015                                      chipcenter(1)