diff --git a/single_cell_analysis_complete_class.ipynb b/single_cell_analysis_complete_class.ipynb index a2423c5..61363fe 100644 --- a/single_cell_analysis_complete_class.ipynb +++ b/single_cell_analysis_complete_class.ipynb @@ -3130,7 +3130,7 @@ " \n", " sc.pp.filter_cells(adata, min_genes=200) #get rid of cells with fewer than 200 genes\n", " #sc.pp.filter_genes(adata, min_cells=3) #get rid of genes that are found in fewer than 3 cells\n", - " adata.var['mt'] = adata.var_names.str.startswith('mt-') # annotate the group of mitochondrial genes as 'mt'\n", + " adata.var['mt'] = adata.var_names.str.startswith('MT-') # annotate the group of mitochondrial genes as 'mt'\n", " adata.var['ribo'] = adata.var_names.isin(ribo_genes[0].values)\n", " sc.pp.calculate_qc_metrics(adata, qc_vars=['mt', 'ribo'], percent_top=None, log1p=False, inplace=True)\n", " upper_lim = np.quantile(adata.obs.n_genes_by_counts.values, .98)\n",