I am analyzing the single cell RNA-seq data generated by our own lab. The whole datasets comprised four time points. My analysis mainly based on Seurat tutorial (https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html). Everything goes fine except for the JackStrawPlot and UMAP. My own jackStrawPlot showed that every component, even PC 20, is highly significant and the many of my clusters in my UMAP plot are not separated well. Below are my JackStrawPlot and UMAP. Is it serious? or normal just different dataset leaded to different plot? Do you have some suggestions?
Thanks in advance.