Reference

Bio::Tradis::AddTagsToSeq(3pm)

Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings.

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 <[email protected]>

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

History