I am using cancer cell line scRNA-seq data to fing rarely expressed cells in homogenous cell culture. I am following seurat vignette for clustering. I also fund the seurat tutorial to regress out cell cycle genes effect. However, I have a basic question. My current work is as follow:
1) Find variable genes
2) Scale data
3) Performed cell cycle scoring analysis
4) Re-scale data with regressing out cell cycle genes effect
5) Run PCA using variable feature generated in step one.
But I am thinking, shouldn't I find out variable genes again if I have made some cell cycle gene based correction, and then run PCA and clustering. Some of the variable genes are cell cycle genes such as TOP2A.
Any comment will be appreciated!