Nature MethodsBioinformaticsPeer-reviewed journal article
Is single nucleus ATAC-seq accessibility a qualitative or quantitative measurement?
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Abstract
Single nucleus ATAC-seq is a key assay for gene regulation analysis. Existing approaches to scoring feature matrices from sequencing reads are inconsistent with each other, creating differences in downstream analysis, and displaying artifacts. We show that even with sparse single cell data, quantitative counts are informative for estimating a cells regulatory state, which calls for consistent treatment. We propose Paired-Insertion-Counting (PIC) as a uniform method for snATAC-seq feature characterization.
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