Is it okay to use a ENSEMBL toplevel genome for mapping when no primary assembly is available?

Question

[Beginner]

Hi,

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?

[lieven.sterck]

I would be very surprised if the reference-assembly for rat would not be in ENSEMBL ? (or is that not what you are looking for?)

https://www.ensembl.org/Rattus_norvegicus/Info/Index

Answer 1

[Beginner]

I just found the answer. In an information file it says "If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent." indicating that the toplevel for rat is equivalent to a primary assembly version of other species such as mouse or human.