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BUTTERFLY: addressi...
BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq
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- Gustafsson, Johan, 1976 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Robinson, Jonathan, 1986 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Nielsen, Jens B, 1962 (author)
- BioInnovation Institute (BII),Chalmers tekniska högskola,Chalmers University of Technology
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- Pachter, Lior (author)
- California Institute of Technology (Caltech)
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(creator_code:org_t)
- 2021-06-08
- 2021
- English.
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In: Genome Biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1474-7596. ; 22:1
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Abstract
Subject headings
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- 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.
Subject headings
- 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)
Keyword
- UMI
- Droplet-based
- Single-cell RNA-Seq
- Correction
- PCR
- Bias
- Amplification
- Batch correction
Publication and Content Type
- art (subject category)
- ref (subject category)
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