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Bio::Tradis::RunTradis(3pm) User Contributed Perl Documentation Bio::Tradis::RunTradis(3pm)

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
2024-01-25 perl v5.38.2