how to export scanpy data to loupe?
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14 months ago
krorange • 0

Hi, I start to use scanpy for analyzing the scRNA-seq and I would like to export the analyzed data to loupe. Is there any tutorial or some suggestions? Thanks!

scRNA scanpy loupe • 773 views
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14 months ago

You mean 10XGenomic's Loupe browser format? I don't think you can. I think it's proprietary.

I asked their techsupport about generating Loupe files from their matrix file formats, and they said it couldn't be done. You will need cellranger, and unless you can see how to make the underlying files that cellranger reanalyze would want, you are going to have to start from scratch.

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oh.. I thought it could be like Seurat that just exporting the x, y coordinates and some other features for Loupe. I tried but I am not that familiar with Python. Thought it was possible to do.

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Those "some other features" would probably be the molecules hd5 files. You'd have to learn their format and make them up from your data in order for cellranger to recognize them and make Loupe files. But in the time it would take you to learn how to do that, you probably could just redo the analysis with cellranger.

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I see. Thank you so much!!

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