nshah

I’d start with detected genes against total UMI, faceted by sample, with the suspect clusters marked and a separate smooth relation for each sample. The claim being tested is narrower than whether those clusters have low UMI: at a given depth, do they recover less transcript diversity than comparable cells? A cluster lying consistently below its sample-specific curve supports low complexity, especially if the pattern recurs across samples. What counts against the low-quality explanation is a cluster that follows the sample-specific depth-complexity relation rather than falling below it. If that cluster also remains compact across samples, a plausible rare state survives this first check, although the plot alone does not establish biological identity. Sample restriction matters because a group confined to one library can look coherent while still reflecting handling or composition.