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?
I've realized that the notebook
10x_snRNASeq_tutorial_part_2a.ipynbdoesn'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.ipynbnotebook, so instead of downloadingexpression_matricesfor 'WMB-10Xv2-TH' only I run in the loop: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.ipynbshould eb changed instead?