ATAC-seq โ Understanding the Scope of "Directly Visualizing Open Chromatin"
Why this matters
ATAC-seq estimates chromatin accessibility by using Tn5 transposase to insert adapters into DNA regions that are accessible, followed by fragment sequencing. Peaks indicate an enrichment of accessibility signals in a specific region; they do not constitute direct evidence of transcription factor binding or gene expression. It is essential to report TSS enrichment, FRiP score, fragment periodicity, library complexity, mitochondrial reads, and replicate concordance. In single-cell ATAC-seq, sparsity, doublets, and batch effects must also be evaluated. QC cutoffs should be interpreted according to the tissue type and protocol used.
Interpretation boundary
This article explains the concept and the limits of the evidence. It does not provide diagnostic, testing, or treatment decisions for an individual patient.