The TSS enrichment score was originally defined by the ENCODE consortium59 as a signal-to-noise metric for ATAC-seq experiments. As the TSS for most genes are typically open, these regions represent a ‘positive control’ set when taken together and enables computing a metric that reflects the sensitivity of the ATAC-seq experiment. The TSS score was defined as the mean number of Tn5 insertion events centered on the TSS sites (±500 bp of the TSS) divided by the mean Tn5 insertion count at TSS-flanking regions, defined as +900 to +1,000 and −900 to −1,000 bp from the TSS. Calculation of the TSS enrichment score per-cell was implemented in the TSSEnrichment function in Signac.
