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velocyto-team / velocyto.R

RNA velocity estimation in R
http://velocyto.org
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Velocyto on single nucleus RNA-seq #97

Open zhanglab2008 opened 4 years ago

zhanglab2008 commented 4 years ago

Hi team, Thank you very much for developing this amazing tool! Do you think Velocyto is suitable for analyzing single nucleus RNA-seq dataset as well? The reason why I ask this is because single nucleus RNA-seq detects larger fraction of unspliced RNAs (e.g. >50% reads mapped to the intronic region) due to the fact that nuclei contain more unprocessed RNAs than whole cells. From the paper, you mentioned that RNA velocity is based on the assumption that "spliced mRNA abundance (RNA velocity) is determined by the balance between production of spliced mRNA from unspliced mRNA, and the mRNA degradation". But for single nucleus RNA-seq, RNAs are unspliced because they are in nucleus. In this case, I wonder if the dynamics of spliced/unspliced RNA can predict a biological process as accurate as it does for single cell. Any comments will be much appreciated. Thanks in advance! Zhang

chatterjee89 commented 3 years ago

I had the same exact question. Following this thread.

FunGeST commented 3 years ago

I have the same question. I am also interested in suggested parameters to run Velocyto on snRNA-seq data. Thanks a lot!

zhanglab2008 commented 3 years ago

there is a discussion here as well. https://github.com/theislab/scvelo/issues/118