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