sub-typing function

[archieandrews10]

Hi Kai:

I was able to integrate snATACseq and snRNAseq data successfully.
I transferred the cell type information from the RNAseq data to the snATACseq data.
Using my marker genes, can I further sub-type the cells with any of the SnapATAC2's built-in functions? If yes, could you point me in that direction?

Thanks
Avinash

[archieandrews10]

Hi Kai,
Any help on this? I predicted the C_scANVI subtype after integrating the scRNAseq. But I want to further subtype the cell that are under C_scANVI based on certain marker genes. I am unable to do using SnapATAC2. Is there a function that I can use?

[kaizhang]

There's no built-in function to do exactly this in SnapATAC2. But you can check with other tools that are designed specifically to analyze transcriptome dataset, e.g., scanpy.