Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

Gustafsson, J.; Robinson, J.; Nielsen, J.; Pachter, L.

doi:10.1101/2020.07.06.188003

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bioRxiv · 10.1101/2020.07.06.188003

Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

Gustafsson, J.·Robinson, J.·Nielsen, J.·Pachter, L.

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Abstract

The incorporation of unique molecular identifiers (UMIs) in single-cell RNA-seq assays allows for the removal of amplification bias in the estimation of gene abundances. We show that UMIs can also be used to address a problem resulting from incomplete sequencing of amplified molecules in sequencing libraries that can lead to bias in gene abundance estimates. Our method, called BUTTERFLY, is based on a zero truncated negative binomial estimator and is implemented in the kallisto bustools single-cell RNA-seq workflow. We demonstrate its efficacy using a range of datasets and show that it can invert the relative abundance of certain genes in cases of a pooled amplification paradox.

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Gustafsson, J., Robinson, J., Nielsen, J., Pachter, L.. 2020-07-06. Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq. https://doi.org/10.1101/2020.07.06.188003

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