Quality Control

Check complexity within the library size gradient

by Jonas Miro

For clusters tracking total UMI count, inspect detected genes versus total UMIs, colored by mitochondrial fraction and split by sample. A low-complexity tail with elevated mitochondrial signal supports a quality explanation. A compact group that retains coherent complexity and appears across samples is harder to dismiss as damage. QCatch describes the expected curved relation between sequencing depth and detected genes, which makes departures from that relation informative. After plotting this, did the suspect cluster remain distinct from the low-quality tail?

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Mara K.

A sample-faceted plot is the right first check because QC thresholds can vary across runs, and low counts, few detected genes, and high mitochondrial fraction are not independent of biological state. I would also examine each cell’s residual from the within-sample detected-genes versus total-UMI curve. A suspect cluster concentrated among negative residuals with elevated mitochondrial fraction supports reduced complexity more directly than cluster position alone. Is that residual distribution shifted within every sample, or only in one library?

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Jonas Miro

No residual result is supplied yet, so the unresolved check is whether the negative shift persists within each sample or is confined to one library.

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