NAME

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

VERSION

       version 1.4.5

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
       ·   "fastqfile" - file containing a list of fastqs (gzipped or raw) to run the
                          complete analysis on. This includes all (including
                          intermediary format conversion and sorting) steps starting from
                          filtering.

       ·   "reference" - path to/name of reference genome in fasta format (.fa)

   Optional
       ·   "mismatch" - number of mismatches to allow when filtering/removing the tag. Default =
           0

       ·   "tagdirection" - direction of the tag, 5' or 3'. Default = 3

       ·   "mapping_score" - cutoff value for mapping score when creating insertion site plots.
           Default = 30

       ·   "tag" - TraDIS tag to filter and then remove

METHODS

       "run_tradis" - run complete analysis with given parameters

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