Bio::Tradis::RemoveTags(3pm)

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 <[email protected]>

COPYRIGHT AND LICENSE

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007