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.
Over the year, there have been several papers asking a similar question, but the definite first step in the analysis is determining what is the 'same gene' usually done via orthologues or paralogues.
Here are some examples on cross species/genus/organism comparisons: