How can Allen transcriptomic identities be assigned to external datasets. For example assigning nuclei from a query dataset as Sst Myh8 vs Sst Chodl?
I have tried using the Allen data as a reference and then mapping my cells onto that reference using Seurat MapQuery. The issue is that this requires clustering the Allen data with Seurat to create the reference and this does not produce the exact same clusters/cell types as the found in the papers. For example, I will get a cluster composed of multiple Sst subtypes (based on the Allen metadata) so when a query cell maps to that cluster I am still not sure what subtype it is.
Is there a better way to do this? Can Scrattch.hitcat do this and if so how?