Error Loading CellBender v3alpha H5 output in R

Hi,

First thanks so much for developing and updating this awesome software! I have been using v2 on Terra for some time and recently saw v3alpha and decided to give that a go (Additional html report is awesome!). However, I’m running into issue loading the data in R using Seurat. Previously I could use Seurat’s Read10X_h5 command. However, now when I do that (either with filtered or full .h5 files I get the following error:

test <- Read10X_h5("/PATH/SampleB_CB_out.h5", use.names = T)
Error in `[[.H5File`(infile, paste0(genome, "/data")) : 
  An object with name droplet_latents/data does not exist in this group

I saw a note in another issue about output of h5 file changing with v3 but didn’t detail how. What is best way to load the v3alpha h5 files in R?

Thanks! Sam

[samuel-marsh]

Hey @sjfleming Sorry for delayed response! Yes V3 alpha seemed to run without any issues (running on Terra)!

I think I will try and submit the primary function to SeuratWrappers in near future (that seems to be their rec for adding new import functions for other formats).

I’ve also created both multi directory and multi-file wrappers in scCustomize as well to read in files from whole experiment (stored in subdirectories or just within one directory) to make things easy for large experiments and add parallelization for additional speed (even though hdf5 files are already pretty quick).

Also added support for examining feature level changes within a dual assay Seurat object https://github.com/samuel-marsh/scCustomize/issues/70#issuecomment-1304047416 (matrix to matrix version coming) (side note it’s great to have this already included in new v3 html report). So this just provides easy wrapper to examine within R/Seurat.

Best, Sam

[samuel-marsh]

Hi,

As fyi, to simplify things on the R end for users I just wrote helper function for my package, scCustomize, to load the counts matrix from new CellBender outputs entirely within R without requiring PyTables. It’s basically slimmed version of Seurat::Read10X_h5 that only reads the matrix.

https://github.com/samuel-marsh/scCustomize/blob/58529b4dc870860c64d5c96eb078f353d7c4ca2b/R/Read_%26_Write_Data.R#L1054

I may update function name and will add it to my other scCustomize CellBender functions vignette. Planning v0.8.0 release for scCustomize by end of the month at latest.

Thanks again, Sam