One read per cell per gene is optimal for single-cell RNA-Seq

M. J. Zhang, V. Ntranos, & D. Tse

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Sep 24, 2018
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Received Date: 6th September 2018

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, the corresponding optimal estimator is not the widely-used plug-in estimator but one developed via empirical Bayes.

Read in full at bioRxiv.

This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.

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