NAME

Bio::Tradis::RemoveTags - Remove tags from seqs 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 Removes tags from the sequence and quality strings Outputs a file *.rmtag.fastq unless an out file is specified

   use Bio::Tradis::RemoveTags;
   
   my $pipeline = Bio::Tradis::RemoveTags->new(fastqfile => 'abc', tag => 'abc');
   $pipeline->remove_tags();

PARAMETERS

Required

• fastqfile - path to/name of file to filter

• tag - TraDIS tag to remove

Optional

• mismatch - number of mismatches to allow when removing the tag. Default = 0

• outfile - defaults to file.rmtag.fastq for and input file named file.fastq

METHODS

remove_tags - output all reads with the tags removed 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