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.
Has this been done before? I am not sure how one would conclude something about evolution by looking at expression levels.
It has been done in maximum 6 species and other organs than my target organ, it is sufficient to get genes which differentially expressed between them to get the change of expression levels between these species in this organ.
If there is a publication can you link it here?
Please use
ADD COMMENT/ADD REPLY
when responding to existing posts to keep threads logically organized.SUBMIT ANSWER
should be used for new answers to original question.https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-313X.2012.05005.x
If I am reading the publication right then the evolution part was analyzed independent of the expression (finding orthologous groups). The groups were then used for co-expression analysis.
I am confused to separate these species to groups or not because I don't know how to select these species in groups; according to the number of replicates or types, and I need an exact pipeline for analyzing.
You could try what the authors of the paper above did:
Thank you so much I will try your suggestion and start with identifying paralogous and orthologous genes.