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 = 0tagdirection
- direction of the tag, 5' or 3'. Default = 3mapping_score
- cutoff value for mapping score when creating insertion site plots. Default = 30tag
- 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