Hi, I am working on an RNA-seq analysis of a wild type and a gamma-irradiated mutant of a non-model organism. The aim is to identify differentially expressed genes between them. So, what I have done is generating 2 separate de novo assemblies, identifying common sequences between the 2 with at least 90% identity using cd-hit-est-2d, and using it as a mapping reference to do DE.
My question is whether my current workflow is fine to be continued or there is any generally accepted workflow to apply in my case? What do you think? Thanks.