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pachterlab / kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data
https://kallistobus.tools/
MIT License
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How to filter/subset cells for RNA Velocity from kb? #32

Closed SimoniMD closed 2 years ago

SimoniMD commented 2 years ago

Hi,

I'm trying to follow the kb/RNA Velocity tutorial listed here but i'm a little confused on how to correlate it with my data.

My steps for analysis were as follows:

  1. Generate counts w/ kb bustools
  2. Load unfiltered counts into R
  3. Use DropletUtils in R to remove empty droplets and create filtered counts
  4. Use Seurat in R to further filter/cluster/further analyze

If I follow the tutorial above, I won't be removing the empty droplets and filtering - so how can I compare the results from the RNA velocity? Also, if i'm only trying to determine the RNA velocity for certain cell types (clusters from Seurat), how would I go about incorporating that? Any insight would be appreciated. Thanks!

SimoniMD commented 2 years ago

Closing this issue for now. Sorry!