amplification – must use native DNA! – Except if using amplified control • DNA-damage repair – Does not impact methylated bases (4-mC, 6-mA, 5-mC) – Avoid for other types of modification (e.g., 8-oxo-G, dU) • Follow large-insert-library template-preparation recommendations for de novo assembly – Compatible with size-selection methods • Optional Tet1-conversion protocol on SampleNet • For resequencing, can use shorter-insert libraries – Proper mapping critical; insert size must exceed the repeat length – Multi-molecule analysis sufficient to perform motif analysis (exception rare DNA- damage events) Experimental Design Isolate DNA Template Preparation Sequencing Analysis