Bio::Tradis::RemoveTags - Remove tags from seqs a fastq file

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

perl v5.38.2                                       2024-01-25                       Bio::Tradis::RemoveTags(3pm)

Methods

       "remove_tags" - output all reads with the tags removed to "outfile"

Name

       Bio::Tradis::RemoveTags - Remove tags from seqs a fastq file

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"

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();