Can I use data based on different genome assemblies?

Hello, I have a question related to this issue. I am using Hisat2 but in the built-in reference genome there is no mm28 only mm9 and mm10. My question Can I select mm10 during Hisat2 and in the next stingtie I use the earlier version mm39 which I uploaded?

Hi @Hossam_Shawki

You will have technical and scientific problems if data based on different genome assemblies are used together in the same analysis. Choose a matching reference genome and reference annotation at the start of an analysis and use those throughout.

Public servers host different genome indexes. hosts mm39 for now.

Note: next time, please consider asking a new question for new problems. You can reference other topics by URL for context.