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no data to run 10x_snRNASeq_tutorial_part_2a #17

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djarecka opened this issue Sep 1, 2023 · 0 comments
Open

no data to run 10x_snRNASeq_tutorial_part_2a #17

djarecka opened this issue Sep 1, 2023 · 0 comments

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@djarecka
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djarecka commented Sep 1, 2023

I've realized that the notebook 10x_snRNASeq_tutorial_part_2a.ipynb doesn't run correctly. The cell 10 with "create empty gene expression dataframe" raise an error, since some files are missing.

I was able to finish the notebook if I change the cell 10 in getting_started.ipynb notebook, so instead of downloading expression_matrices for 'WMB-10Xv2-TH' only I run in the loop:

for key in ['WMB-10XMulti', 'WMB-10Xv2', 'WMB-10Xv3']:
    expression_matrices = manifest['file_listing'][key]['expression_matrices']
    for _, val in expression_matrices.items():
        file_dict = val['log2']['files']['h5ad']
        download_file( file_dict )

However, that downloads 24 h5ad files and it takes quite some time even on kbhub, so perhaps we don't want to change it, and the 10x_snRNASeq_tutorial_part_2a.ipynb should eb changed instead?

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