Scanpy - highest expressed genes
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Entering edit mode
8 weeks ago
mt_pereira • 0

Hello!

I am doing the QC of my scRNA-seq dataset.

I computed the following to get the following commands to display the top 10 genes with the strongest contribution within the counts from the scRNA-seq experiment.

adata_empty.var['frac_gene'] = adata_empty.var['total_counts']*100 / np.sum(adata_empty.var['total_counts'])
adata_empty.var['frac_gene'].sort_values(ascending=False)[:10]

When I computed sc.pl.highest_expr_genes(adata_empty, n_top=10), I expected the same output as the commands above. However, the gene ids were mostly different.

Can anyone help me out understanding what is the difference between both approaches?

Thank you so much in advance!

normalization Scanpy scRNA • 194 views
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