ArticleGenome biology2021
BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed.
- Sequencing saturation does not uniquely determine molecular recovery in UMI transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq.Nature protocols · 2025Review
- kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.bioRxiv : the preprint server for biology · 2024Article
- Multi-batch single-cell comparative atlas construction by deep learning disentanglement.Nature communications · 2023Article
- Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq.Advanced genetics (Hoboken, N.J.) · 2023Review
- Cuproptosis-related molecular subtypes direct T cell exhaustion phenotypes and therapeutic strategies for patients with lung adenocarcinoma.Frontiers in pharmacology · 2023Article
- BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq.Genome biology · 2021Article
- Sources of variation in cell-type RNA-Seq profiles.PloS one · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
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.
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Registered trials
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