Read_10x_h5 Error

Help scanpy
1

I am getting an Error when trying to load a .h5ad file into scanpy:

Exception: File is missing one or more required datasets.

I had a Seurat R object that I converted to a .h5ad file with the R package ‘sceasy’. The conversion seemed to work fine as the output gave a ‘Anndata object’ as shown below:

Screen Shot 2023-04-26 at 3.51.22 pm
Screen Shot 2023-04-26 at 3.51.22 pm969×189 11.5 KB

I am trying to read this into scanpy with the following, but getting the above Error:
adata = sc.read_10x_h5("/path/P2_CD38.h5ad", genome='X')

I am exeprienced with single-cell analyses in R but not python and not sure what to do here. Thanks for any help in advance.

2

Hi, you have to use the read_h5ad() function:
adata = sc.read_h5ad("/path/P2_CD38.h5ad")