Error reading h5seurat file

[yesitsjess]

h5ad_file <- "file.h5ad"
Convert(h5ad_file, dest="h5seurat", overwrite=F)
h5seurat_file <- "file.h5seurat"
seu <- LoadH5Seurat(h5seurat_file, assays="RNA")

Validating h5Seurat file
Initializing RNA with data
Error in sparseMatrix(i = x[["indices"]][] + 1, p = x[["indptr"]][], x = x[["data"]][],  : 
  'dims' must contain all (i,j) pairs

Any advice please?

[usernamekoki]

I have the same question and I use another R package to solve this problem. Its name is "srtdisk". You can get this package through "remotes::install_github("mianaz/seuratdisk-V5")". It helps a lot.

[denvercal1234GitHub]

Also, before importing to R, one would need to convert both adata.obs and adata.var (handles lists, dicts, and categoricals) to string / numeric and ensure to replace in the obs names any / or some unsual characters with _, and ensure that each metadata column to be a single dataset (or a proper categorical with levels + values).

You can check out the anndata_Seurat_Utilities module, which provides the function prepare_adata_for_seurat_drop_empty_v3() to prepare their anndata to input directly in R. See https://github.com/denvercal1234GitHub/anndata_Seurat_Utilities