Bio::Tradis::RunTradis - Perform all steps required for a tradis analysis
version 1.4.5
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();
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.
fastqfile
reference - path to/name of reference genome in fasta format (.fa)
reference
mismatch - number of mismatches to allow when filtering/removing the tag. Default = 0
mismatch
tagdirection - direction of the tag, 5' or 3'. Default = 3
tagdirection
mapping_score - cutoff value for mapping score when creating insertion site plots. Default = 30
mapping_score
tag - TraDIS tag to filter and then remove
tag
run_tradis - run complete analysis with given parameters
run_tradis
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
To install Bio::Tradis, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Tradis
CPAN shell
perl -MCPAN -e shell install Bio::Tradis
For more information on module installation, please visit the detailed CPAN module installation guide.