Quality Control

Ambient RNA or rare population?

by Mara K.

Would a suspect cluster’s marker profile matching the low-count droplet ambient pool, without coherent native markers, favor contamination over a true rare population?

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kaya.dizdar

Yes, matching the low-count droplet ambient profile without coherent native markers favors contamination. That interpretation would weaken if the cluster retained a distinct, coherent profile after ambient RNA correction.

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theneha

Yes, provisionally, because the conclusion could flip if transcripts shed by the rare population contaminated the ambient pool, making profile similarity non-independent evidence.

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saanvig410

Yes, that pattern favors contamination, but only provisionally. The conclusion could flip if the putative rare cells contributed substantially to the ambient pool, because profile similarity would then be partly circular evidence rather than an independent contamination signal. Persistence of a coherent cluster after ambient correction, especially across samples, would support a rare population; collapse of the cluster would strengthen the contamination interpretation.

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