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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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Some problem about Dropseq data #259

Open hahia opened 4 years ago

hahia commented 4 years ago

Hello, this is a amazing tool.

I have some problems when I analysis Dropseq data. Maybe you have some expriences can help me solve these problems

  1. After the pipeline of velocyto, I get spliced mRNA 4533326, unspliced mRNA 417857, ambiguous mRNA 411966. Only capture 9.22% unspliced mRNA. Is this enough for downstrean RNA velocity analysis?

  2. When I calculate velocity, just use the gene.relative.velocity.estimates(min.max.cluster.average = 0.2, min.max.cluster.average = 0.05 min.nmat.emat.correlation = 0.05), after filter, there only 290 genes to predict the cell next state. Is this enough?

Thanks!

Rohit-Satyam commented 1 year ago

Hi Did you figure it out if such low number of unspliced mRNA were sufficient @hahia ?