I've just installed velocyto on python to run some single cell RNAseq analysis. I have previously analysed my 10x data on Seurat and have obtained a count table (in csv) containing only the populations of cells I want to run velocyto on. Looking at the velocyto instructions though it is not obvious to me what argument I should use or how to even pass this count file into velocyto.
If anyone could help that would be great.
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V
1 answer
Unfortunately, this is probably too late to help your situation, but the question is how were those counts generated? If you simply pulled them from the Seurat counts, you will be unable to use them for any RNA Velocity analysis. RNA velocity requires the spliced and unspliced counts, which you can generate using Velocyto or Kallisto Bustools. From there, you could subset these counts based upon the population of cells you were interested in analyzing.
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