NAME

       chipcor - Feature Correlation Tool for ChIP-seq data analysis

SYNOPSIS

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

DESCRIPTION

       chipcor reads a ChIP-seq data file (or from stdin [<]) in SGA  format  (<SGA  file>),  and
       generates  histograms  showing  the  positional  relationship of two features, a reference
       feature (<feature A>) and a target feature (<feature B>) respectively.

       Launching chipcor 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 1.

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

       -h     Show the usage message.

       -w     It indicates the histogram step size (in bp).

       -n <norm>
              Histogram normalization.

              norm = 0 - Raw counts - Histogram bin entries display the product between reference
              and target counts at the corresponding relative distance

              norm = 1 - Count density - Histograms entries are normalized by the total number of
              reference  counts and the window width. The measurement is therefore a target count
              density (per length unit and reference count unit)

              norm = 2 - Global Normalization - Histograms entries are normalized  by  the  total
              number  of  reference  and  target  counts  and  the window width. The curve should
              approach one for large correlation distances (or weak correlation).

              The default value is 0.

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

SEE ALSO

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