8000 missing stringTie ID in gffcomapre tmap file · Issue #88 · gpertea/gffcompare · GitHub
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missing stringTie ID in gffcomapre tmap file #88

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Vermarashi opened this issue Mar 15, 2024 · 1 comment
Open

missing stringTie ID in gffcomapre tmap file #88

Vermarashi opened this issue Mar 15, 2024 · 1 comment

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@Vermarashi
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I used stringtie ballgown pipeline for my data analysis. I am trying to categorize my differentially expressed transcript in novel and known using gffcomapre. During categorization, I found some MSTRGs are marked as semi-novel, some marked as novel, and some are not present in tmap file of gffcompare. So, now I am confused with those MSTRGs which are not present in gffcomapre output.
Should we consider them Novel? If not, how we can validate their categories as novel, semi-novel or known?
@santataRU
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I do not think Gffcompare marks transcripts as novel or semi-novel, do you consider certain transcript classification codes as novel or semi-novel? For example, do you mean code "c" indicating semi-novel?

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@santataRU @Vermarashi
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