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

Title:: Modeling fragment counts improves single-cell ATAC-seq analysis.
Document type:: Article; Journal Article
Author(s):: Martens, Laura D; Fischer, David S; Yépez, Vicente A; Theis, Fabian J; Gagneur, Julien
Abstract:: 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.
Journal title abbreviation:: Nat Methods
Year:: 2024
Journal volume:: 21
Journal issue:: 1
Pages contribution:: 28-31
Fulltext / DOI:: doi:10.1038/s41592-023-02112-6
Pubmed ID:: http://view.ncbi.nlm.nih.gov/pubmed/38049697
Print-ISSN:: 1548-7091
TUM Institution:: Institut für Humangenetik (Prof. Winkelmann)
BibTeX

Occurrences: