NAME

       chipcor - Feature Extraction Tool for ChIP-seq data analysis

SYNOPSIS

       chipscore [ options ] -A <ref feature> -B <tar feature> -b <from> -e <to> [ < ] [ SGA file
       ]

DESCRIPTION

       chipscore reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA  file>),  and
       compares  two  features,  a reference feature (<feature A>) and a target feature (<feature
       B>), with respect to their relative position. It then extract  feature  A  tags  that  are
       enriched in feature B tags according to a given Count Output Threshold or Score (-t).

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

       The feature specification must have the following format: <feature> = <name> [<+|->]

       The strand specification (+|-) being optional.

       The <feature> parameter is a name that corresponds to the second field of  the  SGA  file.
       If no feature is given then all input tags are processed.

       The  SGA  input  file  MUST  BE  sorted by sequence name (or chromosome id), position, and
       strand.  One should check the input SGA file with the following command:

       sort -s -c -k1,1 -k3,3n -k4,4 <SGA file>

OPTIONS

       -A <ref feature>
              The feature that is taken as a reference for correlating chIP-seq tag distances.

              This parameter is mandatory.

       -B <tar feature>
              Tags corresponding to the  target  feature  are  positionally  correlated  to  tags
              corresponding to the reference feature.

              This parameter is mandatory.

       -b <from>
              The  relative  distance  between the two features is analysed within a given range:
              <from> indicates the beginning.

       -e <to>
              The relative distance between the two features is analysed within  a  given  range:
              <to> indicates the end.

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

              This parameter is optional. Its default value is 10.

       -d     Show  debug  info.  The  program performs the sorting order check of the input data
              file.

       -h     Show the usage message.

       -o     Oriented strand option. Requiring oriented strand processing  means  reverting  the
              chromosome axis when the reference feature is on the - strand.

       -r     Reverse extraction process. The program extracts sites that are depleted in feature
              B.

       -q     Report feature B tag counts as 'feature_name=<int>'.

       -t <thres>
              Output threshold or score. The program extracts feature A tags that are enriched in
              feature B tags according to a given count output threshold.

              The default value is 0.

SEE ALSO

       chipcor(1), chipextract(1), chipcenter(1), chippeak(1) chippart(1)