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

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

perl v5.38.2                                       2024-01-25                       Bio::Tradis::TradisPlot(3pm)

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/>

Name

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

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

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();