Hi Community,

I am currently preforming RNA-seq analysis of human dataset and my aim is to find novel transcripts and isoforms. I have aligned the sequences to the reference genome using Hisat2 and assembled the transcripts using Stringtie in both reference guided and de novo methods. When I looked at the number of assembled transcripts I see reference guided mode has assembled twice number of transcripts than de novo method:

stringtie denovo:
exon 400375
transcript 59007

stringtie reference-guided (-G):
exon 708407
transcript 121080

My question is: Is it normal to see this difference and if so what could be the reason?

Thanks in advance.

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