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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Novel transcripts #145

Open sagnikbanerjee15 opened 6 years ago

sagnikbanerjee15 commented 6 years ago

Hello,

I was wondering if there is a way to find novel transcripts solely from the stringtie gtf file output? I was looking at the output and I found some of the transcripts do not have a corresponding "reference_id". Is it correct to consider them as novel transcripts? I also noticed that stringtie produces novel isoforms. I found a gene STRG.8 which was reported to have 3 isoforms. Stringtie could find references for only two isoforms out of the reported 3 isoform. Is this behavior common?

Thank you.

pariyamd commented 2 years ago

Hello,

I was wondering if there is a way to find novel transcripts solely from the stringtie gtf file output? I was looking at the output and I found some of the transcripts do not have a corresponding "reference_id". Is it correct to consider them as novel transcripts? I also noticed that stringtie produces novel isoforms. I found a gene STRG.8 which was reported to have 3 isoforms. Stringtie could find references for only two isoforms out of the reported 3 isoform. Is this behavior common?

Thank you.

Hello Sagnik, I also have the same question. If you came to any conclusions, could you please share your insights? Thanks a lot

sagnikbanerjee15 commented 2 years ago

Hi @pariyamd,

Unfortunately, I do not have an answer for you. We decided to use a different assembler for our work.

Thank you.