Reading in H5AD File from Human Cell Atlas

Question

[Thorerges]

I am trying to import single-cell data from the human cell atlas (e.g, https://www.covid19cellatlas.org/#vento18-10x).

I want to use this files within Seurat, however - I keep getting this error:

> kidney <- ReadH5AD("documents/Datasets/Kidney/")
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: ../../src/hdf5-1.10.0-1/src/H5F.c in H5Fopen(): line 579: unable to open file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: ../../src/hdf5-1.10.0-1/src/H5Fint.c in H5F_open(): line 1208: unable to read superblock
        class: HDF5
        major: File accessibilty
        minor: Read failed

    error #002: ../../src/hdf5-1.10.0-1/src/H5Fsuper.c in H5F__super_read(): line 271: unable to locate file signature
        class: HDF5
        major: File accessibilty
        minor: Not an HDF5 file

    error #003: ../../src/hdf5-1.10.0-1/src/H5FDint.c in H5FD_locate_signature(): line 124: unable to read file signature
        class: HDF5
        major: Low-level I/O
        minor: Unable to initialize object

    error #004: ../../src/hdf5-1.10.0-1/src/H5FDint.c in H5FD_read(): line 217: driver read request failed
        class: HDF5
        major: Virtual File Layer
        minor: Read fai

Any ideas how to read in H5AD files? This has been pretty challenging for me to figure out.

[shohan4me]

Were you able to solve the problem? I am still in the dark trying to figure out!

[Ram]

Please add answers only if you're answering the top level question. If not, use Add Comment or Add Reply as appropriate.

Answer 1

[kthorner]

Hi, ran into the same issue, trying to use data from the same website!

The best workaround I came up with was first converting to the loom format using anndata, and then importing into Seurat with loomR.

I used something similar to the following:

seurat_file = as.Seurat(loom_file, cells="obs_names", features="var_names", normalized="/matrix")

More information here:

https://satijalab.org/seurat/v3.0/conversion_vignette.html

[sanchez231996]

Hi kthorner, I'm having the same issue... how do you converted the h5ad to loop format? I'm not able to find an answer with Seurat vignette

Thanks

[akwong]

You can use the anndata python package and the write_loom function

adata = anndata.read("stewart19_adult.processed.gzip.h5ad")
adata.write_loom("stewart19_adult.processed.gzip.h5ad.loom")

Answer 2

[Eijy Nagai]

Hello,

It is quite late, but I also ran into the same question and couldn't find a better discussion.

I've tried several methods including the solution presented here (anndata.read/write_loom) but it didn't work on the dataset I was trying ("Haniffa_PBMC").

The solution that worked for me is described here, using the function Convert from SeuratDisk.

Convert("pbmc3k_final.h5ad", dest = "h5seurat", overwrite = TRUE)

Then you can load:

pbmc3k <- LoadH5Seurat("pbmc3k_final.h5seurat")

[ye.liu]

Hi Nagai,

This works for me.

Thank you!