velociraptor preparation
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Pietro ▴ 30
@pietro-13029
Last seen 5 months ago
Italy

Hi,

I would like to use velociraptor package to compute RNA velocity.

I have obtained the .loom object with velocyto for a sample for which I already have the SingleCellExperiment object.

Is it just adding spliced and unspliced matrix to the assay slot of my existing sce object? If so, do you have commands on how to do that?

Thanks,

Pietro

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ATpoint ★ 1.2k
@atpoint-13662
Last seen 4 hours ago
Germany

See the RNA velocity chapter in OSCA for starters: http://bioconductor.org/books/3.14/OSCA.advanced/trajectory-analysis.html#rna-velocity

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Thanks, I have seen that. But my point was more to how to go from velocyto loom output to the spliced and unspliced assay in the SingleCellExperiment object.

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assay(sce, "spliced") <- spliced_counts
assay(sce, "unspliced") <- unspliced_counts


Do you mean something like this? Please be more clear at exactly what step you have issues. Is it extracting the counts from the loom file?