Spatial transcriptomics data
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6 months ago
lsudupe ▴ 10

I just started working with seurat and I'm trying to read spatial transcriptomic data. Until now I work with .h5 files so I didn't have any trouble loading my data but now, I'm trying to load this studyes data (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163629) and I can't create any seurat object to work with.

I have a file with the image, a metadata file and count_matrix. I have been trying a lot of ways and I can go further. Can someone help me? I tried to transform to anndata in scanpy, try to transform to .h5 file in seurat and scanpy... I don't know what or how to do it.

Thanks!!

seurat scanpy no-visium .h5 spatial • 823 views
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6 months ago
Pratik Mehta ▴ 700

Hi,

I found this tool/documentation:

https://rdrr.io/github/MarioniLab/DropletUtils/man/write10xCounts.html

I think that should allow to convert to the h5 format.

And then after you would follow the Seurat documentation for loading 10x spatial datasets:

https://satijalab.org/seurat/reference/load10x_spatial

Specifically, where it says:

data.dir    Directory containing the H5 file specified by filename and the image data in a subdirectory called spatial

Good luck and hope this helps!

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Thank you very much!!!

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