Few arrows or chaotic arrows. What are the key parameters when analyze loom files?

[Suger0917]

Dear velocyto team, The spliced and unspliced model is really excellent! I have been testing your method for three weeks, but can't produce good results. Our project is about the development of an organ. And out data is consist of 2000+ cells with 5000 gene number and 100,000 UMI in average. The ratio of spliced and unspliced molecules is 80% and 17%. I followed the analysis pipeline but got few arrows. If I set the 'quiver_scale ' and 'min_pass' as a really small number, I got chaotic arrows. vlm.plot_grid_arrows(scatter_kwargs_dict={"alpha":0.5, "lw":1, "edgecolor":"0.4", "s":80, "rasterized":True}, min_mass=0.1, angles='xy', scale_units='xy', headaxislength=2.75, headlength=5, headwidth=4.8, quiver_scale=0.005, scale_type="absolute") If I used unspliced prediction, I got no arrows.Could you please give me some advice?

When I use Monocle2, I have to set the start state. But I am not sure about the start state of my project, I think RNA velocity is the right method for this project. I really need your professional guidance!!! Please help me!!!

[ChelseaCHENX]

Hi! I was having similar issues - when using constant velocity assumptions I can get dots without arrows and when using constant unspliced I get even not dots at all.

One possible reason I can think of is the survived unspliced gene number is too few - before filtering, it is 0.2 * 30000 = 6000 but after filtering it is 0.15 * 3000 = 450. Do you think this could be the cause? The sample of mine is not a developing tissue but just normal cell lines in culture - is this kind of less dynamic sample types unsuitable for velocity analysis considering sensitivity etc issues?

Thanks!