Question: Running scVelo on Seurat
1
gravatar for V
5 days ago by
V230
UK/London
V230 wrote:

Hello,

I’m trying to run scVelo on my dataset but I’m running into some issues and was wondering if you could help me.

I have done my analysis on Seurat, and have subset and re-analysed sub-clusters and would like to run scVelo on those sub-clusters. Im trying to run it following this pipeline :

https://github.com/basilkhuder/Seurat-to-RNA-Velocity#generating-loom-files

The issue is I’ve stumbled on the first step. Is it possible to generate a loom file from Seurat that scVelo would accept and if so would you be able to give an example code of how? Trying the as.loom function in R on the subset Seurat object is being temperamental. Velocyto has been very glitchy and since this is analysis on a subcluster I’m not sure how it would need to be run as the 10x files contain all the cells and I’m only interested in a subpopulation of those.

Thank you, and sorry for the naive question.

ADD COMMENTlink written 5 days ago by V230

I get this error when attempting "as.loom"

Error in loomR::create(filename = filename, data = data[feature.order,  : 
  unused arguments (feature.attrs = as.list(x = meta.feature), transpose = TRUE, calc.count = FALSE, max.size = max.size, verbose = verbose)

Have updated my Hdf5r and LoomR....

ADD REPLYlink written 5 days ago by V230
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