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mojaveazure / seurat-disk

Interfaces for HDF5-based Single Cell File Formats
https://mojaveazure.github.io/seurat-disk
GNU General Public License v3.0
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Trying to convert h5ad file to h5seurat and producing file in directory but cannot open #129

Open mwu2001 opened 2 years ago

mwu2001 commented 2 years ago

I've been trying to convert an h5ad file to an h5seurat file so I can work with it in R with Seurat.

Convert("my_directory/file_clustered.h5ad", dest = "h5seurat", assay = "RNA", overwrite = FALSE, verbose = TRUE) which led to:

Screen Shot 2022-10-03 at 10 34 38 AM

This produced, though unclear if corrupted, a respective .h5seurat file. I tried to open this with: seuratObj <- LoadH5Seurat("my_directory/file_clustered.h5seurat") which led to this error:

Screen Shot 2022-10-03 at 10 36 33 AM

Not quite sure what to do and have been dealing with this for >2 weeks. Would appreciate any direction or help!

coarfa commented 2 years ago

I second this. If using the newer version of AnnData eg 0.8 or 0.9, then SeuratDisk cannot parse it properly. At the moment we are dealing with this by forcing an older version of anndata, but hopefully SeuratDisk will be able to tell and handle appropriately newer versions of the AnnData format.

Thank you for this great package otherwise, it was very helpful in our work.

ElenaSLuis commented 1 year ago

I am using AnnData version: ‘0.7.5.5’ and I have the same issue