Error reading HDF5 file in MuData/AnnData

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1

Hi,
I’m attempting to read the following CITE-seq dataset from an HDF5 file (the raw feature / cell matrix hdf5 file), but encounter an error when reading it with anndata.read_h5ad and mudata.read_h5mu both complaining about an unexpected keyword matrix in the hdf5 file.

Has anyone encountered this error with 10X assays? Does Anndata/Mudata expects some specific format of hdf5 keys to parse that this deviates from?

2

Hey @ors,

I think the answer might be that this is the count matrix rather than a MuData/AnnData file so it might be muon.read_10x_h5 or scanpy.read_10x_h5 that you’re looking for.

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3

That works, thanks a lot!

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