RNA velocity on 5' 10x data?
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2.2 years ago
Lucy ▴ 80

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

RNA-Seq scRNA-seq RNA velocity • 3.6k views
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Is 10x not 3' end data?

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The Single Cell Gene Expression kits are 3', but the Single Cell Immune Profiling gene expression data is 5'.

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2.2 years ago

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.

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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.

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Great thanks. I thought it would be because it also uses poly(T) priming but I hadn't seen anyone mention it, so I just wanted to check before I tried.

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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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