I am working with RNA-seq data and I have identified circRNA on them. Know I want to do the differential expression analysis. I am wondering which kind of normalization should I perform on the circRNA I have identified to perform the differential expression.
As circRNA identification tools try to identify a junction read of the circularization, my guess is that there is no need to take into account the gene length for the normalization. As it is only taken into account the fusion junction read. Would it be correct just to use tags per million?
Thank you very much