I am working on microbial genomics, and there are a couple of datasets in SRA/ENA that I can use for my work. I want to combine these datasets in a single study but the problem is these datasets are all done on different subspecies of S. aureus.
I tried creating a common reference genome annotation according to a methodology by LoVerso and Cui - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668955/, but it mapped only around 200 genes in common between two species.
Is there any other method wherein I can map the homologs of a second genome to the primary reference annotation and carry out an integrated analysis in a single go? (Because that creates many numbers of replicates under the same condition and increases the reliability of the studies)
Or am I supposed to do separate differential expression for each dataset and then compare the obtained genes separately?