Modeling fragment counts improves single-cell ATAC-seq analysis.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 38049697.
- Also identified by DOI 10.1038/s41592-023-02112-6 and PMC identifier 10776385.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Chromatin Immunoprecipitation Sequencing
- High-Throughput Nucleotide Sequencing