BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

Gustafsson, Johan,1976Chalmers tekniska högskola,Chalmers University of Technology (författare)

The incorporation of unique molecular identifiers (UMIs) in single-cell RNA-seq assays makes possible the identification of duplicated molecules, thereby facilitating the counting of distinct molecules from sequenced reads. However, we show that the naïve removal of duplicates can lead to a bias due to a “pooled amplification paradox,” and we propose an improved quantification method based on unseen species modeling. Our correction called BUTTERFLY uses a zero truncated negative binomial estimator implemented in the kallisto bustools workflow. We demonstrate its efficacy across cell types and genes and show that in some cases it can invert the relative abundance of genes.

Robinson, Jonathan,1986Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)jonrob (författare)
Nielsen, Jens B,1962BioInnovation Institute (BII),Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)nielsenj (författare)
Pachter, LiorCalifornia Institute of Technology (Caltech) (författare)
Chalmers tekniska högskolaBioInnovation Institute (BII) (creator_code:org_t)

Ingår i:Genome Biology: Springer Science and Business Media LLC22:11474-760X1474-7596

Av författaren/redakt...: Gustafsson, Joha ...; Robinson, Jonath ...; Nielsen, Jens B, ...; Pachter, Lior

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