How to normalise counts to compare RNAseq results between two spcecies

Question

[LDT]

Dear all,

I am looking for advice. I have two closely related species, and I want to compare the RNA expression of the same organ between species. Does anyone know how to normalise the data and compare these values?

I have found these interesting paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2745-1

I appreciate your time

[Lada]

Hi!

I am going through all the posts related to cross-species transcriptomics because I have a similar goal in my research so I was wondering how did the analysis go so far for you since I planned on following the methodology from the same paper. I am pretty much new to bioinformatics so I am struggling at the moment with the basics such as making an expression matrix, but I managed to run SCBN in R on test data and get the p-values.

Thank you so much!

Answer 1

[Istvan Albert]

You should follow that process if you have a paper on this subject.

In general, very few people embark on such a study; After all, one might observe substantial variability even when redoing an analysis on the same data from the same species with a different method or functional enrichment code. The additional parameter space brought in by having to reconcile the two transcriptomes adds another dimension to the problem.

That is not to say that interesting observation could not be made in a cross-species comparison - just that it is more difficult to pursue.

Long story short, I would follow the exact methodology described in the paper as it provides credibility and precedent.