I used to work with ENSEMBL genomes for differential gene expression. A new dataset is now in a species (rat) that does not have a primary assembly file, only toplevel. I normally used the primary assembly.
I think it is fine, but just wanted to make sure that there won't be any major issues for DEG analysis when I use the toplevel genome for mapping. Or is there a way to get a primary assembly file for rat from ENSEMBL?