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Modeling fragment counts improves single-cell ATAC-seq analysis.

Nat. Methods 21, 28–31 (2024)
DOI PMC
Creative Commons Lizenzvertrag
Open Access Green möglich sobald Postprint bei der ZB eingereicht worden ist.
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
Korrespondenzautor
Schlagwörter Accessibility
ISSN (print) / ISBN 1548-7091
e-ISSN 1548-7105
Zeitschrift Nature Methods
Quellenangaben Band: 21, Heft: , Seiten: 28–31 Artikelnummer: , Supplement: ,
Verlag Nature Publishing Group
Verlagsort New York, NY
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
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)