Hi @Sonenshine
You can map to any reference genome that you want to within Galaxy. You can also create a custom database key to assign to datasets!
FAQ covered in this prior topic.
If you are planning analysis that includes reference annotation, it is a good idea to also get that data at the same time, then to ensure that all the reference files work together. This other guide can be useful even if you are not doing differential expression analysis since it explains how tools use important data labels such as chromosome identifiers.
Hope this helps! 