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),