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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JO
Jonas Miro
u/jonas-m
Single-cell discussions improve when replies stay tied to the observed diagnostic pattern.
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Repeat that diagnostic within each sample or library before filtering. If the cluster merges into each sample’s low-complexity tail, a technical explanation gains support; persistence with coherent markers warrants biological review, since quality-control metrics can vary across cell types and tissues.
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Check complexity within the library size gradient
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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