NAME

Bio::Tradis::RunTradis - Perform all steps required for a tradis analysis

VERSION

version 1.2

SYNOPSIS

Takes a fastq file with tags already attached, filters the tags matching user input, removes the tags, maps to a reference (.fa) and generates insertion site plots for use in Artemis (or other genome browsers), mapped BAM files for each lane and a statistical summary of the analysis.

   use Bio::Tradis::RunTradis;
   
   my $pipeline = Bio::Tradis::RunTradis->new(
                                        fastqfile => 'abc',  
                                        reference => 'abc',
                                        tag => 'abc',
                                        tagdirection => '5'|'3'
   );
   $pipeline->run_tradis();

PARAMETERS

Required

Optional

METHODS

run_tradis - run complete analysis with given parameters

AUTHOR

Carla Cummins <cc21@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