ATAC-seq and the Nextera workflow are designed for sequencing using Illumina high-throughput sequencing instruments. When sequencing ATAC-seq libraries, Nextera-based sequencing primers and reagents must be used. Depending on the sequencing instrument, this may require modification of the standard sequencing workflow. For nucleosome mapping, paired-end sequencing is preferred. Paired-end 50-cycle reads generally provide accurate alignments with reasonable costs. For inferring differences in open chromatin within human samples we generally use >50M mapped reads and for transcription factor foot-printing we use >200M mapped reads (Neph et al., 2012). Data yield can sometimes be impacted by the large fraction of mitochondrial reads. For troubleshooting cluster densities and sequencing quality refer to Illumina’s technical support staff.
