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)

Bioinformatics                                      July 2015                                         chipcor(1)