Questions on house keeping genes:

What are good house keeping genes to use with Patch-Seq?

Should we be using housekeeping genes to normalize data?

Can we use NormFinder to find good house keeping genes?

We don’t typically use housekeeping genes for normalization of single cell RNA-seq data (Patch-Seq or otherwise). Please see this response about Patch-seq normalization, and a more general post about data normalization here. All that said, I am unfamiliar with “NormFinder” and can’t comment on its general utility.