Andrey Prjibelski comments

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                                            Andrey Prjibelski

Swiping on a macOS mouse ought to pan rather than zoom

Agree, will fix as well.

spades-core: /opt/conda/conda-bld/spades_1664217775513/work/src/project/spades/main.cpp:101: int main(int, char**): Assertion `cfg::get().K >= runtime_k::MIN_K && cfg::get().K < runtime_k::MAX_K' failed.finished abnormally, OS return value: -6

Dear @GuillaumeDore11 This looks quite odd, since 127 is the maximal possible value and there are multiple checks for that. Is it possible you SPAdes version was modified by someone?...

Bug: missing transcript annotations (present by StringTie)

Dear @sarahcalvo IsoQuant is sometimes overly careful as the main goal is to maintain high precision, which sometimes causes recall drops. Thanks for the report, I will look into the...

TPM value difference of a sample between runs

Dear @abhijitcbio I don't see any errors in your command lines. Here are a few comments: - If you are looking for expression of reference transcripts, I'd suggest using `*.transcript_tpm.tsv`....

TPM value difference of a sample between runs

IsoQuant 3.4 is released, so I suggest to give it a try.

TPM value difference of a sample between runs

I'll close this issue for now, please, re-open if needed.

JSONDecodeError while running

Dear @abhijitcbio This is quite odd, as JSON configs are created and loaded by the same library. It may be possible that there is some discrepancies between different IsoQuant versions...

JSONDecodeError while running

Please, reopen if this issue still appears in 3.4.2.

Dear @francicco Thanks for the feedback! > First, which of the two gtf should I take as a final annotation extended_annotation.gtf or transcript_models.gtf? For my understanding the first, extended_annotation.gtf, Because...

Issue in identifying 3′ end position

Dear @seungbeom-han Yes, the is a problem with respect to transcripts ends that is on our TODO list. When IsoQuant assigns reads to known isoforms it does account for difference...