Whole genome bisulphite sequencing using the Illumina X system [ATAC-Seq]

While Illumina X technology has helped to reduce the cost of whole genome sequencing substantially, its application for bisulphite sequencing is not straightforward. We describe the optimization of a library preparation and sequencing approach that maximizes the yield and quality of sequencing, and how to eliminate a previously unrecognized artefact affecting several percent of bisulphite sequencing reads. Overall design: The accessible regions of chromatin from ENCODE tier 1 cell line GM12878 were assayed from two different cultures; thus, producing two biological replicates.