Overlapping cluster/annotation

Question

[synat.keam]

Dear Senior Fellows,

I used Seurat to cluster my single cells and use singleR for annotation, but there seems to be an overlapping cluster / annotation. Are they doublets? or just error with annotation (circle in red). if they are doublets, is there any standard workflow in seurat I could remove them from seurat object! thank you before hand.

Kind Regards,
Synat,

Answer 1

[LChart]

I don't see any colored points corresponding to those labels (no yellow dots under "Chondrocytes", nothing looking green near "HSC_-G-CSV". What are the proportion/counts of these cell types in the overall dataset? If they're <1% of the total; I'd consider removing or reannotationg potentially. Or is this a subset of a much larger pool of cells (i.e., one donor from an experiment with dozens?)