Merged seurat objects, clustering problem, help please

Question

[rmorabar]

Hello, I have 3 cancer seurat objects (all of them same cancer), which I worked separately until only having immune cells (i already removed all mitocondrial, ribosomal and IgG genes from these databases). Also, I removed all the unnecessary metadata, resolutions and graphs name. After that I merged all seurat objects, compared the genes names across all datasets, and retained only the common ones (overlap.genes). Run JoinLayers, NormalizedData, RunPCA, RunUMAP. After I checked that I needed to do batch correction, so did harmony. Now that I want to do Findneighbors and FindClusters, the clustree gives me a lot of clusters, even at resolution zero.

I dont know what is happening. Have any of you had this issue before?

[ATpoint]

Impossible to say just based on your description. Try working on the textual description, show diagnostic plots and relevant code.