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How should overlapper handle N's? #86

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samhunter opened this issue Jul 28, 2017 · 6 comments
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How should overlapper handle N's? #86

samhunter opened this issue Jul 28, 2017 · 6 comments
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@samhunter
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Should N's match other N's?
How does overlapper deal with Ns?
Should overlapper subtract the quality value associated with an N, or just use the overlapped base + qual score?

@dstreett
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I'll chime in on what it currently does (though I am not sure I agree with it).

To start the alignment, the kmer profiling treats N's like its own base. So, kmers with N's in them are considered, however, there needs to be an exact string match between the two reads (N's included) to initiate the overlap.

N's are currently treated on par with the other bases. So if a 'N' mismatches with a 'A' the algorithm will take the highest q score still (hopefully it is the A). Additionally, it will subtract the qscores just as if N was normal base.

@msettles What are your thoughts?

@dstreett dstreett reopened this Jul 28, 2017
@msettles
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msettles commented Jul 29, 2017 via email

@msettles
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Any movement on this? Can it be closed?

@msettles msettles reopened this Oct 15, 2017
@samhunter
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I'm not sure, going to have to let David comment.

I think we did end up having one difference from your version of the approach above. For matching bases, I think we are adding q-scores with a ceiling of 40. This improves qualities for low-quality ends that overlap and match.

@msettles
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msettles commented Oct 19, 2017 via email

@msettles
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2+ years later going to go ahead and close

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