NAME

       chippart - Partitioning Tool for ChIP-seq data analysis

SYNOPSIS

       chippart  [ options ] -f <feature name> -p <transition penalty> -s <density threshold> [ <
       ] [ SGA file ]

DESCRIPTION

       chippart reads a ChIP-seq data file (or from stdin [<]) in SGA format  (<SGA  file>),  and
       finds  signal-enriched  regions across the whole file for ChIP-tag positions corresponding
       to a specific feature <feature name>, or all features.

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

       The  <feature>  parameter  is a name that corresponds to the second field of the SGA file.
       It might optionally include the strand specification (+|-).  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>

       The output is an SGA-formatted list containing the regions of interest.

       The  program  also  generates  (to  stderr)  a  statistical  report  with  the   following
       information:

         - Total number of processed sequences, total DNA length, and
           total number of fragments;
         - Total length of fragments, average fragment length, and
           percentage of total DNA length;
         - Percentage of total counts, average number of counts, and
           number of count per bp (count density).

OPTIONS

       -c <cut-off>
              A value can be 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.

       -f <feature name>
              This parameter is used to select all or a sub-set  of  chIP-seq  input  tags.   The
              feature name is specified in the second field of the SGA-formatted input file.

              If no feature name is given, then all features are selected.

       -h     Show the usage message.

       -p <transition penalty>
              It  assigns  a (negative) score to a transition between signal-enriched and signal-
              poor regions. This parameter needs to  be  negative.   It  therefore  controls  the
              fragment length, i.e high penalty -> long fragments.

              This parameter is mandatory.

       -s <density threshold>
              A  region must have a count density higher than the value specified by the <density
              threshold> in order to be considered as a signal-enriched DNA stretch.

              This parameter is mandatory.

SEE ALSO

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