I want to compare Multiple vertebrate species RNA seq data(more than 11 species) in the same organ to realize the transcriptome evolution between them in the target Organ, I have the alignment files of these species, I must point out that there are different replicates per species(e.g. 4 rep for Bos, 6rep for Mus, 1 rep for Macaca)
I'm completely new to this field and I need bits of advice to make a most accurate pipeline for my analysis.
Any advice is valuable to me.
Thanks a lot in advance.