# Error reading HDF5 file in MuData/AnnData

**URL:** <https://discourse.scverse.org/t/error-reading-hdf5-file-in-mudata-anndata/3272>\
**Category:** anndata\
**Created:** [September 30, 2024, 4:01pm UTC](https://discourse.scverse.org/t/error-reading-hdf5-file-in-mudata-anndata/3272 "2024-09-30T16:01:06Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ors](https://avatars.discourse-cdn.com/v4/letter/o/df788c/32.png) [@ors](https://discourse.scverse.org/u/ors)\
**Post date:** [September 30, 2024, 4:01pm UTC](https://discourse.scverse.org/t/error-reading-hdf5-file-in-mudata-anndata/3272/1 "2024-09-30T16:01:06Z")

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Hi,  
I’m attempting to read the following [CITE-seq dataset](https://www.10xgenomics.com/datasets/10-k-cells-from-a-malt-tumor-gene-expression-and-cell-surface-protein-3-standard-3-0-0) 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?

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**Author:** ![gtca](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/gtca/32/1199_2.png) [@gtca](https://discourse.scverse.org/u/gtca)\
**Post date:** [September 30, 2024, 9:29pm UTC](https://discourse.scverse.org/t/error-reading-hdf5-file-in-mudata-anndata/3272/2 "2024-09-30T21:29:11Z")

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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`](https://muon.readthedocs.io/en/latest/io/input.html#id2) or [`scanpy.read_10x_h5`](https://scanpy.readthedocs.io/en/stable/generated/scanpy.read_10x_h5.html) that you’re looking for.

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<div class="post-metadata">

**Author:** ![ors](https://avatars.discourse-cdn.com/v4/letter/o/df788c/32.png) [@ors](https://discourse.scverse.org/u/ors)\
**Post date:** [October 6, 2024, 9:20am UTC](https://discourse.scverse.org/t/error-reading-hdf5-file-in-mudata-anndata/3272/3 "2024-10-06T09:20:28Z")

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That works, thanks a lot!