table of contents
Bio::Tradis::FilterTags(3pm) | User Contributed Perl Documentation | Bio::Tradis::FilterTags(3pm) |
NAME¶
Bio::Tradis::FilterTags - Filter tags in a fastq file
VERSION¶
version 1.4.5
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 = 0
- "outfile" - output file name. Defaults to "file.tag.fastq" for an input file named "file.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
2020-01-11 | perl v5.30.0 |