what is the .h5ad file?

[fenghuijian]

Hi,
I have some question about the .h5ad file .
What is a h5ad file?
What is its data storage structure?
Why is it read much faster than CSV.

[Koncopd]

Hi, this is a hdf5 file with some additional structure specifying how to store AnnData objects.
We use h5py package, so you can read more about the hdf5 file format there.

[josinejansen]

Hi Koncopd,
Do you happen to know how to re-write an .h5ad file to a 'regular' .h5 file? Or to directly sc.write_10x_h5 ?
I'd like to execute some downstream analyses with a subset of cells I created with Anndata/Scanpy, using a software package which can not read the .h5ad format, but CAN however read the .h5 format.

The issue was discussed before, but was wondering if in the mean time other people ran into this problem & whether there are some updates [https://github.com/scverse/scanpy/issues/262]

Thanks in advance,
Josine

[Koncopd]

Hi, @josinejansen . You can open a h5ad file as if it is a standard hdf5 file.