why in RNA seq don't we only use reference transcriptome? I would like to ask why in RNA seq analysis (alignment step) we use sometimes reference genome instead of reference transcriptome? thank you!
Pseudoaligmnent to a reference transcriptome with something like Kallisto is perfectly valid, assuming you are in an organism whose reference transcriptome is very well documented.
But if you want to find novel transcripts or novel splicing junctions, you need to align to genome.