How to set the 'expected_doublet_rate' in Scrublet?

swolock / scrublet

Detect doublets in single-cell RNA-seq data

MIT License

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How to set the 'expected_doublet_rate' in Scrublet? #30

Open victorwang123 opened 3 years ago

victorwang123 commented 3 years ago

As I follow the Chromium User Guidehttps://support.10xgenomics.com/permalink/3vzDu3zQjY0o2AqkkkI4CC However, the number of my samples greatly beyond it, (e.g. One sample had 21546 cells), I want to know how to set the 'expected_doublet_rate'? it seems set typically 0.05-0.1

swolock commented 3 years ago

The doublet rate should scale linearly with the number of cells loaded, so based on the user guide, I'd expect a doublet rate of ~0.15 for your sample with ~21k cells.

Getting the expected doublet rate exactly right is not essential – just be sure to look at the doublet score histograms to set an appropriate threshold.