The length of DNA wrapped around a single nucleosome has been experimentally determined as 147 bp57. As Tn5 has a strong preference to integrate into nucleosome-free DNA58, successful ATAC-seq experiments typically exhibit a depletion of DNA fragments with lengths that are multiples of 147 bp. We defined the nucleosome signal QC metric in Signac as the ratio of mononucleosomal (147–294 bp) to nucleosome-free (<147 bp) fragments sequenced for the cell, as a way of quantifying the expected depletion of nucleosome-length DNA fragments. To compute the nucleosome signal per cell, we sampled the first n fragments from the fragment file, where n was the total number of cells in the dataset multiplied by 5,000. We then divide the number of mononucleosomal fragments per cell by the number of nucleosome-free fragments. This was implemented in the NucleosomeSignal function in Signac.
