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)