Library sequencing Sequence the library and correlate reads with open and closed chromatin. When sequencing ATAC-seq libraries, sequencing primers and reagents must be used. For nucleosome mapping, paired-end sequencing is preferred. Foe inferring differences in open chromatin with human samples,we generally use>50,000,000 mapped reads, and for transcription factor foot-printing, we use>200,000,000 mapped reads. The mitochondrial read fraction can vary between 10% and >50%, depending on cell type.