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Rationale for using old salmon version #80

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tycho-kirchner opened this issue Apr 17, 2024 · 0 comments
Open

Rationale for using old salmon version #80

tycho-kirchner opened this issue Apr 17, 2024 · 0 comments

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@tycho-kirchner
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tycho-kirchner commented Apr 17, 2024

Hi,
I've noticed that SalmonTE still uses the rather old salmon version v0.8.2 and I would kindly like to ask for the rationale to do so. The newer version v1.10.0 runs much faster on my system, however, I've noticed much more mapping artifacts, where all (or most) reads of highly repetitive transcripts are assigned to locus A in sample S1, but to locus B in sample S2. Possible related issues are here and here

Do you have any thoughts on that?
Thanks and kind regards
Tycho

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