Hi,
I was wondering whether RNA velocity (https://www.nature.com/articles/s41586-018-0414-6) can be used on 5' 10x scRNA-seq data and whether the results are similar to that achieved with 3' 10x data?
Many thanks,
Lucy
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Lucy •
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Yes, why couldn't it be? As for whether it's comparable, I'm sure there are differences, but I expect that general trends would hold true. You can always give it a shot and see whether it works for your data - it is fairly easy to run via scvelo or velocyto, which also has a Seurat wrapper if you use that.
FYI you can now run RNA velocity with three commands: $ pip install kb-python $ kb ref -d linnarsson -i idx.idx -t t2g.txt -c1 t2c_cDNA.txt -c2 t2c_intron.txt $ kb count --lamanno --filter --h5ad -i idx.idx -g t2g.txt -x 10xv2 -c1 t2c_cDNA.txt -c2 t2c_intron.txt R1.fastq.gz R2.fastq.gz
See https://pypi.org/project/kb-python/ for more info.
The prerequisite to analyzing RNA velocity is obtaining splicing metrics. However, due to extremely low sequencing depth and coverage, some papers point current 10x data can hardly be used to analyze the splicing phenomenon. I'm curious how could it be possible to analyze RNA velocity using 10x data? How about the performance? Thanks.
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