Provided by: bio-tradis_1.4.5+dfsg2-1_all
Bio::Tradis::FilterTags - Filter tags in a fastq file
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();
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"
"filter_tags" - outputs all reads containing the provided tag to "outfile"
Carla Cummins <firstname.lastname@example.org>
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