I was engaged with a basic problem. I have dataset consist ~2000 cells and composed 8-9 clusters using Seurat package, then I transfer Seurat object to the Monocle.
I tried monocle2 and monocle3. The problem is, how to make the trajectory ?
If I choose a cluster as a starting point, I might put bias on the data, and also if we let the package select the starting point and the path it might not be the proper start and point ?
My question is, what is the best way to make the pseudo-time trajectory ? Using Seurat object directly or giving cell and gene expression information ?