Issues with RNA Velocity Analysis Between Subpopulations of One Cell Type
I am working on an RNA velocity analysis for one cell type which has 4 different subpopulations (based on whether they are high or low expression aka +/- for 2 different genes). My PI believes these genes are important based on wet lab experiments.
I'm following the scVelo tutorial to do this but my trajectories and positions are all over the place.
I tried placing around with the # of highly variable genes (below is 2000), I did basic filtering, and my unspliced counts are between the 10-25% they recommend. I also only have 1000 cells so perhaps this is an issue but I can't fix this part as we were given this data. Any other ideas I can try?
Sorry if this is a strange question but I am happy to answer any clarifying questions as well. Thank you guys in advance.
However when I try an RNA velocity tutorial from scVelos