H5py file

[menage95]

Hello thank you for this amazing resource!
I just wanted to ask how processed the expression matrix from the file is? I want to recluster the midbrain data but didn't know which steps to include e.g. filtering/normalisation?

Thanks!
Lucy

[slinnarsson]

Hi & thanks. It is unprocessed raw UMI counts, but only cells that passed QC are included. Hence, you should start over from the beginning but you don't need to remove doublets etc.