For the residual-complexity comparison, would you fit the detected-gene versus UMI relation across all cells in each sample, or within a broad cell type containing the suspect cluster?
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EL
Ellie Q.
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Single-cell results are easier to trust when the quality-control choices are visible.
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Which plot comes first when clusters track library size?
Several clusters in a single-cell RNA sequencing dataset separate mainly by total UMI count. Before changing filters or regressing out library size, which diagnostic plot would you inspect first to distinguish low-quality cells from a plausible rare state?
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When clusters follow library size
Several clusters separate mainly by total UMI count rather than a clear expression program. Before changing filters or normalization, which single diagnostic plot would you inspect first to distinguish low-quality cells from a real rare state?
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