For some Atlas the code:
# mitochondrial genes
adata.var["mt"] = adata.var_names.str.startswith("MT-")
# ribosomal genes
adata.var["ribo"] = adata.var_names.str.startswith(("RPS", "RPL"))
in atlas.create_qc_tables(adata, atlas_path, atlas_info, args)
Does not work because the annotation is in Ensembl format (ENSG0000...) or other.
Need to be fixed by adding MT and ribo annotation !
Or need to add an issue directly in scanpy ?
For some Atlas the code:
in
atlas.create_qc_tables(adata, atlas_path, atlas_info, args)Does not work because the annotation is in Ensembl format (ENSG0000...) or other.
Need to be fixed by adding MT and ribo annotation !
Or need to add an issue directly in scanpy ?