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Determining sequencing depth in a single-cell RNA-seq experiment
An underlying question for virtually all single-cell RNA sequencing experiments is how to allocate the limited sequencing budget: deep sequencing of a few cells or shallow sequencing of many cells? Here we present a mathematical framework which reveals that, for estimating many important gene proper...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005864/ https://www.ncbi.nlm.nih.gov/pubmed/32034137 http://dx.doi.org/10.1038/s41467-020-14482-y |
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author | Zhang, Martin Jinye Ntranos, Vasilis Tse, David |
author_facet | Zhang, Martin Jinye Ntranos, Vasilis Tse, David |
author_sort | Zhang, Martin Jinye |
collection | PubMed |
description | An underlying question for virtually all single-cell RNA sequencing experiments is how to allocate the limited sequencing budget: deep sequencing of a few cells or shallow sequencing of many cells? Here we present a mathematical framework which reveals that, for estimating many important gene properties, the optimal allocation is to sequence at a depth of around one read per cell per gene. Interestingly, the corresponding optimal estimator is not the widely-used plug-in estimator, but one developed via empirical Bayes. |
format | Online Article Text |
id | pubmed-7005864 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-70058642020-02-10 Determining sequencing depth in a single-cell RNA-seq experiment Zhang, Martin Jinye Ntranos, Vasilis Tse, David Nat Commun Article An underlying question for virtually all single-cell RNA sequencing experiments is how to allocate the limited sequencing budget: deep sequencing of a few cells or shallow sequencing of many cells? Here we present a mathematical framework which reveals that, for estimating many important gene properties, the optimal allocation is to sequence at a depth of around one read per cell per gene. Interestingly, the corresponding optimal estimator is not the widely-used plug-in estimator, but one developed via empirical Bayes. Nature Publishing Group UK 2020-02-07 /pmc/articles/PMC7005864/ /pubmed/32034137 http://dx.doi.org/10.1038/s41467-020-14482-y Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Zhang, Martin Jinye Ntranos, Vasilis Tse, David Determining sequencing depth in a single-cell RNA-seq experiment |
title | Determining sequencing depth in a single-cell RNA-seq experiment |
title_full | Determining sequencing depth in a single-cell RNA-seq experiment |
title_fullStr | Determining sequencing depth in a single-cell RNA-seq experiment |
title_full_unstemmed | Determining sequencing depth in a single-cell RNA-seq experiment |
title_short | Determining sequencing depth in a single-cell RNA-seq experiment |
title_sort | determining sequencing depth in a single-cell rna-seq experiment |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005864/ https://www.ncbi.nlm.nih.gov/pubmed/32034137 http://dx.doi.org/10.1038/s41467-020-14482-y |
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