Related Experiment Video
Updated: Jul 9, 2025
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
Modeling fragment counts improves single-cell ATAC-seq analysis
Laura D Martens1,2,3, David S Fischer2,4, Vicente A Yépez1
1School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
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.
