Doublets in scRNAseq analysis

Question

[Binghong]

Hello, I am trying to analyze scRNAseq data in R and have identified a subset of B cells that co-express CD3D and CD19, indicating doublets. However, even after removing doublets using doubletfinder, I still find these doublets present. Should I directly remove this group of cells that co-express CD3D and CD19, or are there better alternatives, as I am concerned about the presence of other doublets? Any guidance is appreciated!

Answer 1

[OmnibusX]

I often see a small population of B cells expressing CD3D in scRNAseq data, and I also do find some papers discussing this phenomenon. I suggest you check the number of transcripts, and genes of cells from this population. If they are not abnormally high, you might consider them as a special subpopulation of B cells in your data.

[Binghong]

Thanks for your suggestions! I will check it!