NAME

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

VERSION

version 1.3.2

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

• 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.

• tag - TraDIS tag to filter and then remove

• 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

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