8000 Can transcripts from the same gene be classified as 'x' and 'u' by GffCompare? · Issue #101 · gpertea/gffcompare · GitHub
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Can transcripts from the same gene be classified as 'x' and 'u' by GffCompare? #101

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RafaellaFerraz opened this issue Apr 19, 2025 · 0 comments
Open

Can transcripts from the same gene be classified as 'x' and 'u' by GffCompare? #101

RafaellaFerraz opened this issue Apr 19, 2025 · 0 comments

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@RafaellaFerraz
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I'm working with RNA-seq data and performed transcriptome assembly using StringTie, followed by classification with GffCompare. I'm observing something puzzling: some transcripts that appear to originate from the same gene locus are being classified differently — some as x (antisense) and others as u (intergenic). From my understanding, 'x' indicates overlap with a known gene on the opposite strand, while 'u' means the transcript is intergenic. So, I was wondering:

  • Is it biologically or technically possible for the same gene locus to produce both 'u' and 'x' transcripts?
  • Could this be an artifact of transcript assembly or a reflection of complex transcriptional regulation?

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