DOKK / manpages / debian 12 / bio-tradis / Bio::Tradis::TradisPlot.3pm.en
Bio::Tradis::TradisPlot(3pm) User Contributed Perl Documentation Bio::Tradis::TradisPlot(3pm)

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

version 1.4.5

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();

"mappedfile" - mapped and sorted BAM file

  • "outfile" - base name to assign to the resulting insertion site plot. Default = tradis.plot
  • "mapping_score" - cutoff value for mapping score. Default = 30

"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/>

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

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
2020-01-11 perl v5.30.0