NAME

Bio::Tradis::AddTagsToSeq - Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.

VERSION

version 1.4.5

SYNOPSIS

Bio::Tradis::AddTagsToSeq parses BAM files, adds given tags to the start of the sequence and creates temporary SAM file, which is then converted to BAM

   use Bio::Tradis::AddTagsToSeq;
   
   my $pipeline = Bio::Tradis::AddTagsToSeq->new(bamfile => 'abc');
   $pipeline->add_tags_to_seq();

NAME

Bio::Tradis::AddTagsToSeq

PARAMETERS

Required

bamfile - path to/name of file containing reads and tags

Optional

outfile - name to assign to output BAM. Defaults to file.tr.bam for an input file named file.bam

METHODS

add_tags_to_seq - add TraDIS tags to reads. For unmapped reads, the tag is added to the start of the read sequence and quality strings. For reads where the flag indicates that it is mapped and reverse complemented, the reverse complemented tags are added to the end of the read strings. This is because many conversion tools (e.g. picard) takes the read orientation into account and will re-reverse the mapped/rev comp reads during conversion, leaving all tags in the correct orientation at the start of the sequences in the resulting 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