Forum:Steps after doublet detection in single cell data

Question

[ishwarvh]

Hello,

I was wondering how everyone here deals with doublets. I used DoubletFinder on already clustered single cell data. DoubletFinder predicted that there are about ~8% doublets, and about 50% of them are part of 2 tiny clusters and another 50% are interspersed in the rest of the clusters.

I was wondering what is the consensus about the steps after doublet detection?

1. Do you remove the predicted doublets and stick with the existing clusters and proceed to marker identification?

2. Remove the predicted doublets and re-analyze the data starting with the raw count matrix of the singlets?

Appreciate any inputs you may have.

Thanks