Can't read output h5 file about cellbender HOT 3 CLOSED

Thanks for the quick reply Stephen. h5ls is just a generic HDF5 list function from R rhdf5 package. I don't quite understand why I was able to read other h5 files but not cellbender. Anyhow, I went back to the basics after your reply and it turns out I was missing system library libhdf5-dev. After installing it, I am now able to read in cellbender output into Seurat.
Thanks for doing a great work supporting the package!
Vinko

from cellbender.

Hi @vtosevski , thanks for trying it out. Glad the tool ran okay for you. For loading and working with the data, there are a couple of options. Two of the methods (scanpy and pytables) are mentioned here

https://cellbender.readthedocs.io/en/latest/getting_started/remove_background/index.html#use-output-count-matrix-in-downstream-analyses

I'd recommend loading the data in scanpy for any downstream work.

import scanpy as sc

# load the data
adata = sc.read_10x_h5('cellbender_out_filtered.h5')

But if you just want to take a look at the h5 file itself, I'd recommend pytables, using something like

import tables

with tables.open_file('cellbender_out_filtered.h5') as f:
    print(f)  # display the structure of the h5 file

However, I do not know why the method you tried didn't work. I am not familiar with h5ls, so I'm not sure I can be super helpful with debugging the command you tried.

from cellbender.

Hi Vinko, thanks so much for posting that here, hopefully it can also help others who run into this issue!

from cellbender.