Do I need to remove doublets after before or after running hashsolo?

Question

[bioinfo]

Hello,

I have a sample that contains hashtags. I did QC using scanpy and then I used sce.pp.hashsolo to demultiplex the hashtags. I was wondering if I need to remove the doublets from the data. Normally I use scrublet for that but I am not sure if I should do QC then scrublet then hashsolo or if I should use scrublet after hashsolo. I also see that hashsolo includes a doublet output so I am not sure if I should remove those cells from the sample.

Thank you

Answer 1

[tothepoint]

IMO after initial QC, it's a good practice to run Scrublet as it can help ensure that the demultiplexing process is not get false positive outcome by the presence of doublets, which might be incorrectly assigned or affect the assignment of cell barcodes.