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AS, ZS and NH tags: semantics? #49
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Reiner, was this ever addressed? |
Hi Rick, I do not know. I have not recently used hisat to see if Daehwan addressed this. Best, Reiner |
Reiner,
I did a bit more digging.
They appear to have addressed some of these issue with later releases.
They did acknowledge that NH gave incorrect values.
Now I just have to find out how they calculate their alignment scores :)
Dr Rick Tearle
Senior Bioinformatician
Davies Research Centre
University of Adelaide Roseworthy Campus
rick.tearle@adelaide.edu.au
+61 432 07 58 07
From: rschulzUK <notifications@github.com<mailto:notifications@github.com>>
Reply-To: infphilo/hisat2 <reply@reply.github.com<mailto:reply@reply.github.com>>
Date: Friday, 20 October 2017 at 18:14
To: infphilo/hisat2 <hisat2@noreply.github.com<mailto:hisat2@noreply.github.com>>
Cc: Rick Tearle <rick.tearle@adelaide.edu.au<mailto:rick.tearle@adelaide.edu.au>>, Comment <comment@noreply.github.com<mailto:comment@noreply.github.com>>
Subject: Re: [infphilo/hisat2] AS, ZS and NH tags: semantics? (#49)
Hi Rick,
I do not know. I have not recently used hisat to see if Daehwan addressed this.
Best, Reiner
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Dear Daehwan,
I stumbled across two cases (see below) where I am unclear about whether I either incorrectly interpret the tags or they are indeed inconsistent. Hisat2 version and invocation were:
Based on the definition from the Hisat2 web site,
ZS:i:<N> Alignment score for the best-scoring alignment found other than the alignment reported. [...]
, I understand ZS to refer to the best-scoring alignment among the other found alignments, which could be greater than AS. However, I am confused by the additional sentenceNote that, when the read is part of a concordantly-aligned pair, this score could be greater than [AS:i].
. Why can ZS only be greater than AS when the read is part of a concordantly-aligned pair?NH is defined as
The number of mapped locations for the read or the pair.
Does the use oflocations
instead ofalignments
imply that distinct alignments spanning the same coordinates in the target genome are not counted here? That could explain case 1 below, but not case 2.Any help with understanding this would be much appreciated.
Case 1: ZS is present, suggesting that there are >1 alignments, but NH=1.
Case 2: NH=2, but ZS is not present.
Best, Reiner
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