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

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