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

       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

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

       "run_tradis" - run complete analysis with given parameters

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

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

       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();

       version 1.4.5