Question: RNA velocity on 5' 10x data?
0
gravatar for Lucy
10 months ago by
Lucy40
Lucy40 wrote:

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 rna velocity scrna-seq • 1.4k views
ADD COMMENTlink modified 10 months ago by jared.andrews077.2k • written 10 months ago by Lucy40

Is 10x not 3' end data?

ADD REPLYlink written 10 months ago by kristoffer.vittingseerup3.4k
1

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

ADD REPLYlink modified 10 months ago • written 10 months ago by Lucy40
1
gravatar for jared.andrews07
10 months ago by
jared.andrews077.2k
Memphis, TN
jared.andrews077.2k wrote:

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.

ADD COMMENTlink written 10 months ago by jared.andrews077.2k
2

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.

ADD REPLYlink written 10 months ago by Lior Pachter530

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.

ADD REPLYlink written 10 months ago by Lucy40
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