Thanks for your comment. The number of cell type I'm expecting are 18 major ones and the clustering cover this; for some of them I have subtypes all clustered, for some others not, and for some major cell type while for example I expect 5 subpopulations it gives 2 or 3 which confuse me what should I do. subpopulations are more than 40s. When I do clustering without using stability tools and increase the resolution it results in many subpopulation of oligodendrocyte that are not what I want or expected. What do you recommend in this situation? should I do subset and sub cluster?
I also used scDblFinder and excluded about 15k of my cells
Many thanks, Paria