Bio::T...gsToSeq(3pm)

🌸 Bio::Tradis::AddTagsToSeq 💅

okay bestie, so this whole page is about Bio::Tradis::AddTagsToSeq (the manpage header calls it Bio::T...gsToSeq(3pm) because manpage names get truncated, it's giving mysterious but it's literally just this module). It takes a BAM file and makes a brand new BAM with tr and tq tags added onto the sequence and quality strings. Iconic behaviour, no cap.

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✨ VERSION ✨

version 1.4.5 — she's a specific girl, respect her.

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🦋 SYNOPSIS 🦋

So Bio::Tradis::AddTagsToSeq parses BAM files, adds the tags you give it to the start of the sequence, and creates a temporary SAM file, which then gets converted to BAM. That's the whole pipeline, bestie.

use Bio::Tradis::AddTagsToSeq;

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

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💖 NAME 💖

Bio::Tradis::AddTagsToSeq — that's her, that's the name, periodt.

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🎀 PARAMETERS 🎀

Required (you HAVE to bring these, fr fr)

• bamfile — path to / name of the file containing the reads and the tags. Not optional, don't try it.

Optional (nice to have 🫶)

• outfile — the name you want to give the output BAM. If you don't say anything, it defaults to file.tr.bam for an input file named file.bam. She'll name it for you, she's thoughtful like that.

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🔥 METHODS 🔥

• add_tags_to_seq — adds the TraDIS tags to the reads.

Here's the tea though, because the two cases are not the same:

• 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.

Why, you ask? Because many conversion tools (e.g. picard) take the read orientation into account and will re-reverse the mapped/rev comp reads during conversion — which leaves all the tags in the correct orientation at the start of the sequences in the resulting FastQ file. It's giving galaxy brain. 💅

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🌈 AUTHOR 🌈

Carla Cummins <path-help@sanger.ac.uk> — shoutout to the queen who wrote this. 👑

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👑 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

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and that's the whole page, bestie 💜 this was perl v5.30.0, dated 2020-01-11, and it's filed under Bio::T...gsToSeq(3pm). go add some tags, you got this ✨🦋🎀