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Martens, L.D. ; Fischer, D.S. ; Yépez, V.A.* ; Theis, F.J. ; Gagneur, J.

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

Nat. Methods 21, 28–31 (2024)
Publ. Version/Full Text DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
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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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Accessibility
ISSN (print) / ISBN 1548-7091
e-ISSN 1548-7105
Journal Nature Methods
Quellenangaben Volume: 21, Issue: , Pages: 28–31 Article Number: , Supplement: ,
Publisher Nature Publishing Group
Publishing Place New York, NY
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Grants 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)