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Open Access Green möglich sobald Postprint bei der ZB eingereicht worden ist.
Modeling fragment counts improves single-cell ATAC-seq analysis.
Nat. Methods 21, 28–31 (2024)
Single-cell ATAC sequencing coverage in regulatory regions is typically binarized as an indicator of open chromatin. Here we show that binarization is an unnecessary step that neither improves goodness of fit, clustering, cell type identification nor batch integration. Fragment counts, but not read counts, should instead be modeled, which preserves quantitative regulatory information. These results have immediate implications for single-cell ATAC sequencing analysis.
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Publikationstyp
Artikel: Journalartikel
Dokumenttyp
Wissenschaftlicher Artikel
Schlagwörter
Accessibility
ISSN (print) / ISBN
1548-7091
e-ISSN
1548-7105
Zeitschrift
Nature Methods
Quellenangaben
Band: 21,
Seiten: 28–31
Verlag
Nature Publishing Group
Verlagsort
New York, NY
Nichtpatentliteratur
Publikationen
Begutachtungsstatus
Peer reviewed
Institut(e)
Institute of Computational Biology (ICB)
Förderungen
European Union
Helmholtz Association's Initiative and Networking Fund through Helmholtz AI
Deutsche Forschungsgemeinschaft
Helmholtz Association under the joint research school Munich School for Data Science
Deutsche Forschungsgemeinschaft (German Research Foundation)
Helmholtz Association's Initiative and Networking Fund through Helmholtz AI
Deutsche Forschungsgemeinschaft
Helmholtz Association under the joint research school Munich School for Data Science
Deutsche Forschungsgemeinschaft (German Research Foundation)