NAME

       Bio::Tradis::TradisPlot - Generate plots as part of a tradis analysis

VERSION

       version 1.4.5

SYNOPSIS

       Generate insertion plots for Artemis from a mapped fastq file and a reference in GFF
       format

          use Bio::Tradis::TradisPlot;

          my $pipeline = Bio::Tradis::TradisPlot->new(mappedfile => 'abc');
          $pipeline->plot();

PARAMETERS

   Required
       "mappedfile" - mapped and sorted BAM file

   Optional
       ·   "outfile" - base name to assign to the resulting insertion site plot. Default =
           tradis.plot

       ·   "mapping_score" - cutoff value for mapping score. Default = 30

METHODS

       "plot" - create insertion site plots for reads in `mappedfile`. This file will be readable
       by the Artemis genome browser <http://www.sanger.ac.uk/resources/software/artemis/>

AUTHOR

       Carla Cummins <path-help@sanger.ac.uk>

COPYRIGHT AND LICENSE

       This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

       This is free software, licensed under:

         The GNU General Public License, Version 3, June 2007