I’m trying to run scVelo on my dataset but I’m running into some issues and was wondering if you could help me.
I have done my analysis on Seurat, and have subset and re-analysed sub-clusters and would like to run scVelo on those sub-clusters. Im trying to run it following this pipeline :
The issue is I’ve stumbled on the first step. Is it possible to generate a loom file from Seurat that scVelo would accept and if so would you be able to give an example code of how? Trying the as.loom function in R on the subset Seurat object is being temperamental. Velocyto has been very glitchy and since this is analysis on a subcluster I’m not sure how it would need to be run as the 10x files contain all the cells and I’m only interested in a subpopulation of those.
Thank you, and sorry for the naive question.