EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays
Abstract Multiomic droplet-based technologies allow different molecular modalities, such as chromatin accessibility and gene expression (scATAC-seq and scRNA-seq), to be probed in the same nucleus. We develop EmptyDropsMultiome, an approach that distinguishes true nuclei-containing droplets from bac...
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BMC
2024-05-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-024-03259-x |
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| author | Stathis Megas Valentina Lorenzi John C. Marioni |
| author_facet | Stathis Megas Valentina Lorenzi John C. Marioni |
| author_sort | Stathis Megas |
| collection | DOAJ |
| description | Abstract Multiomic droplet-based technologies allow different molecular modalities, such as chromatin accessibility and gene expression (scATAC-seq and scRNA-seq), to be probed in the same nucleus. We develop EmptyDropsMultiome, an approach that distinguishes true nuclei-containing droplets from background. Using simulations, we show that EmptyDropsMultiome has higher statistical power and accuracy than existing approaches, including CellRanger-arc and EmptyDrops. On real datasets, we observe that CellRanger-arc misses more than half of the nuclei identified by EmptyDropsMultiome and, moreover, is biased against certain cell types, some of which have a retrieval rate lower than 20%. |
| format | Article |
| id | doaj-art-dc7e5b4fb0f44f3ba80919314a8e35b3 |
| institution | OA Journals |
| issn | 1474-760X |
| language | English |
| publishDate | 2024-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-dc7e5b4fb0f44f3ba80919314a8e35b32025-08-20T02:18:35ZengBMCGenome Biology1474-760X2024-05-0125111510.1186/s13059-024-03259-xEmptyDropsMultiome discriminates real cells from background in single-cell multiomics assaysStathis Megas0Valentina Lorenzi1John C. Marioni2European Molecular Biology Laboratory European Bioinformatics InstituteEuropean Molecular Biology Laboratory European Bioinformatics InstituteEuropean Molecular Biology Laboratory European Bioinformatics InstituteAbstract Multiomic droplet-based technologies allow different molecular modalities, such as chromatin accessibility and gene expression (scATAC-seq and scRNA-seq), to be probed in the same nucleus. We develop EmptyDropsMultiome, an approach that distinguishes true nuclei-containing droplets from background. Using simulations, we show that EmptyDropsMultiome has higher statistical power and accuracy than existing approaches, including CellRanger-arc and EmptyDrops. On real datasets, we observe that CellRanger-arc misses more than half of the nuclei identified by EmptyDropsMultiome and, moreover, is biased against certain cell types, some of which have a retrieval rate lower than 20%.https://doi.org/10.1186/s13059-024-03259-xMultiomicsSingle-cellMethod |
| spellingShingle | Stathis Megas Valentina Lorenzi John C. Marioni EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays Genome Biology Multiomics Single-cell Method |
| title | EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays |
| title_full | EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays |
| title_fullStr | EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays |
| title_full_unstemmed | EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays |
| title_short | EmptyDropsMultiome discriminates real cells from background in single-cell multiomics assays |
| title_sort | emptydropsmultiome discriminates real cells from background in single cell multiomics assays |
| topic | Multiomics Single-cell Method |
| url | https://doi.org/10.1186/s13059-024-03259-x |
| work_keys_str_mv | AT stathismegas emptydropsmultiomediscriminatesrealcellsfrombackgroundinsinglecellmultiomicsassays AT valentinalorenzi emptydropsmultiomediscriminatesrealcellsfrombackgroundinsinglecellmultiomicsassays AT johncmarioni emptydropsmultiomediscriminatesrealcellsfrombackgroundinsinglecellmultiomicsassays |