I am using Seurat 3.1 to integrate my 11 samples (2 Knock-out, 3 wild type 3 Knock-in and 3 Overexpression) via standard workflow. The results of UMAP seemed ill-defined and unclear:
In another attempt, I also tried tSNE, but the result also look weird:
I tried to set different dims and the result didn't improve. So could you please tell me how improve the result of tSNE and UMAP when using Seurat 3.1? Thanks a million in advance.