NAME

       chipextract - Feature Correlation and Extraction Tool for ChIP-seq data analysis

SYNOPSIS

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

DESCRIPTION

       chipextract reads a ChIP-seq data file (or from stdin [<])  in  SGA  format  (<SGA  file>)
       containing  two features, a reference feature (<feature A>) and a target feature (<feature
       B>), correlates the genomic tag count distributions for the two  features,  and  for  each
       reference  feature,  it  extracts  target  feature  tags  that  fall into a distance range
       ([from,to]) relative to the reference feature.

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

       The feature specification must have the following format:

       <feature> = <name> [<+|-|0[strandless]|a[any]|o[oriented]>]

       Accepted  strand  values  are the following: +|-|0[strandless]|a[any]|o[oriented].  If the
       strand is not specified, it is set to a[any] by default.

       The <feature> parameter is a name that corresponds to the second field of the SGA file.

       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>

       The  output  is  a  table  in text format consisting of all reference features (rows) with
       relative target tag counts in bins of a given size defined by <window> width (columns).

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 target feature 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) or bin.

SEE ALSO

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