One read per cell per gene is optimal for single-cell RNA-seq.
under review in Nature Communications, 2018 (joint work with Martin Zhang* and David Tse)
An underlying question for virtually all single-cell RNA sequencing experiments is how to allocate the limited sequencing budget: deep sequencing of a few cells or shallow sequencing of many cells? A mathematical framework reveals that, for estimating many important gene properties, the optimal allocation is to sequence at the depth of one read per cell per gene. Interestingly, our analysis shows that the corresponding optimal estimator is not the widely-used plug-in estimator but one developed via empirical Bayes.