Genotype-free demultiplexing of pooled single-cell RNA-seq.
- Xu J Genome Innovation Hub, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Falconer C Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Nguyen Q Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Crawford J Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- McKinnon BD Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Mortlock S Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Senabouth A Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute, 384 Victoria St, Darlinghurst, Sydney, NSW 2010, Australia.
- Andersen S Genome Innovation Hub, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Chiu HS Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Jiang L Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Palpant NJ Genome Innovation Hub, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Yang J Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Mueller MD Department of Obstetrics and Gynaecology, Berne University Hospital, Bern, 3012, Switzerland.
- Hewitt AW Department of Surgery, The University of Melbourne, Parkville, 3010, Australia.
- Pébay A Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, 3010, Australia.
- Montgomery GW Genome Innovation Hub, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
- Powell JE UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
- Coin LJM Genome Innovation Hub, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia. lachlan.coin@unimelb.edu.au.
- 2019-12-21
Published in:
- Genome biology. - 2019
Allele fraction
Demultiplexing
Doublets
Expectation-maximization
Genotype-free
Hidden Markov Model
Machine learning
Unsupervised
scRNA-seq
scSplit
Humans
Sequence Analysis, RNA
Single-Cell Analysis
Software
English
A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling. We introduce scSplit which utilizes genetic differences inferred from scRNA-seq data alone to demultiplex pooled samples. scSplit also enables mapping clusters to original samples. Using simulated, merged, and pooled multi-individual datasets, we show that scSplit prediction is highly concordant with demuxlet predictions and is highly consistent with the known truth in cell-hashing dataset. scSplit is ideally suited to samples without external genotype information and is available at: https://github.com/jon-xu/scSplit.
- Language
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- English
- Open access status
- gold
- Identifiers
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- DOI 10.1186/s13059-019-1852-7
- PMID 31856883
- Persistent URL
- https://folia.unifr.ch/global/documents/58124
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