NAME
Bio::Tradis::FilterTags - Filter tags in a fastq file
VERSION
version 1.3.3
SYNOPSIS
Reads in a fastq file with tradis tags already attached to the start of the sequence Filters reads that contain the provided tag Outputs a file *.tag.fastq unless an alternative outfile name is specified
use Bio::Tradis::FilterTags;
my $pipeline = Bio::Tradis::FilterTags->new(fastqfile => 'abc', tag => 'abc');
$pipeline->filter_tags();
PARAMETERS
Required
fastqfile
- path to/name of file to filter. This may be a gzipped fastq file, in which case a temporary unzipped version is used and removed on completion.tag
- TraDIS tag to match
Optional
mismatch
- number of mismatches to allow when matching the tag. Default = 0outfile
- output file name. Defaults tofile.tag.fastq
for an input file namedfile.fastq
METHODS
filter_tags
- outputs all reads containing the provided tag to outfile
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