table of contents
Bio::Tradis::TradisPlot(3pm) | User Contributed Perl Documentation | Bio::Tradis::TradisPlot(3pm) |
NAME¶
Bio::Tradis::TradisPlot - Generate plots as part of a tradis analysis
VERSION¶
version 1.4.5
SYNOPSIS¶
Generate insertion plots for Artemis from a mapped fastq file and a reference in GFF format
use Bio::Tradis::TradisPlot; my $pipeline = Bio::Tradis::TradisPlot->new(mappedfile => 'abc'); $pipeline->plot();
PARAMETERS¶
Required¶
"mappedfile" - mapped and sorted BAM file
Optional¶
- "outfile" - base name to assign to the resulting insertion site plot. Default = tradis.plot
- "mapping_score" - cutoff value for mapping score. Default = 30
METHODS¶
"plot" - create insertion site plots for reads in `mappedfile`. This file will be readable by the Artemis genome browser <http://www.sanger.ac.uk/resources/software/artemis/>
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
2020-01-11 | perl v5.30.0 |