I'm interested in calculating isoform abundance in a certain tissue, and be able to compare the abundance between human patients / mouse.
From what I can tell my best option is : (1) to use methods (such as RSEM) that quantify the isoforms using known annotations of the genome and isoforms, because both genomes should be well annotated. (2) then use a method based on splicing events (such as MISO) or isoforms (such as EBSeq/cuffdiff) to compare the abundance. In this step both options looks problematic. Any recommendation for such a method, that will work well with quantification methods? or other thoughts? I have access to raw data if it matters.
Have you trying using MATS? Or if you don't mind having alternative exon expression instead of alternative isoforms, then you can try DEXSeq
haven't tried DEXseq or MATS yet, but I would prefer working with isoforms, not alternative exons.
Each exon would be annotated by its gene name
so beyond all the isoforms which are already there in reference gtf, if you get alternative exon usage then that would denote alternate isoform also