I am doing single nuclei analysis on brain neurons (inhibitory and excitatory) and glia cells using Seurat. The UMAP is like below showing clustering results. The clusters in the middle are sticking together.
I have tried changing dims in FindNeighbors and resolution in FindClusters, but still cannot separate the chunk in the middle.
Is there anything I am doing incorrectly? Or it is because they are neurons and glia, so they might be quite similar and cannot be separated?
integrated5<- FindNeighbors(integrated3, reduction = 'pca', dims = 1:11) integrated5<- FindClusters(integrated5, resolution = 0.5) integrated5<- RunUMAP(integrated5, reduction = 'pca', dims=1:11)
In the upstream, I integrated 12 subjects' data. I believe there is no batch effect?
Please bear with here there plots look not so pretty...