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 could you please, help me in understanding the reason or refer to any article.
Thanks in advance.