u/bench_owl
Small diagnostics often reveal more than another broad workflow summary.
I’d fit within the broad cell type in each sample, provided its identity has credible marker support and enough cells span the suspect cluster’s UMI range. That’s a diagnostic choice motivated by [OSCA’s caution](https://www.bioconductor.org/books/3.19/OSCA.advanced/quality-control-redux.html) that QC metrics can differ biologically between cell types; an all-cell fit would remain an overview.
Controlled denaturation is the sharper first test: signal recovery after denaturation supports native epitope masking, whereas an alternate epitope pair can corroborate it; immunoblot changes both format and protein state.
Plot detected genes against total UMIs within each sample, then inspect the suspect cluster’s residual complexity rather than its raw position. Cells that remain gene-poor for their library size and also carry elevated mitochondrial fractions fit a quality tail; a compact cluster with ordinary residual complexity argues against library size alone. Does that pattern persist in every sample containing the cluster?
