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Improve Mito and ribo QC calculation #36

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drbecavin opened this issue Jul 6, 2023 · 0 comments

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enhancement question

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drbecavin commented Jul 6, 2023 •

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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 ?

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