Label transfer between 10x and pipseq

[brianFSM]

Has anyone here had success in transferring cell-type labels from a reference dataset generated using 10x over to a pipseq dataset of the same tissue? I'm concerned that the data are not actually compatible. I'm deep in an analysis trying to pull this off, but it's not working very well. There aren't a lot of variable features overlapping between the two datasets, and most of the query cells end up being labeled as fibroblasts, which doesn't match what the marker genes are suggesting. Thanks!