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.