Guidelines for typical chemistries

10x Genomics

10xV3

10x genomics V3 chemistry for feature barcoding is using a mapping between RNA cell barcodes and Protein cell barcodes. You can find this mapping here

Since the list is composed of ~7M cells instead of the ~3M described in the technologie, using the whitelist of V3 as an input is unwise. I suggest running CITE-seq-Count with using the -cells argument instead.