ScVelo using merged loom or individual loom ?

[meghamsh738]

Hello, Thanks for the awesome package.

I have question on the pipeline. There are multiple ways to make velocities from the data. Which one to choose for correct interpretation?

Briefly,

1. Merge data -> Merge loom -> Run ScVelo
2. Merge data -> Separate individual data with the same UMAP embeddings-> Run loom separately on each data
3. Integrate data -> Merge loom -> Run ScVelo

Thanks !