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

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

Robinson, Jonathan, 1986 (författare): Chalmers tekniska högskola,Chalmers University of Technology

Nielsen, Jens B, 1962 (författare): BioInnovation Institute (BII),Chalmers tekniska högskola,Chalmers University of Technology

(creator_code:org_t)

2021-06-08
2021
Engelska.
Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1474-7596. ; 22:1

Relaterad länk:: https://research.cha... (primary) (free); visa fler...; https://genomebiolog...; https://doi.org/10.1...; https://research.cha...; visa färre...

Abstract Ämnesord

Stäng

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.

NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)

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

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