Illumina sequencing and data processing

Library construction was performed using the KAPA Hyper Prep kit as described in the manual (https://www.kapabiosystems.com/), with the only exception that five PCR cycles post-adaptor ligation libraries were size-selected for mononucleosomes, i.e., 200–400 bp using BluePippin (Sage Science) (Supplemental Fig. S3). qPCR was performed to determine the additional PCR cycles needed for optimal library concentration. Paired-end 100 bp Illumina HiSeq sequencing was performed at the University of California, Davis, DNA technologies core facility. Demultiplexing, adaptor, and quality trimming of the raw reads was performed using the Allprep script (https://github.com/Comai-Lab/allprep). Paired reads were merged using SeqPrep (https://github.com/jstjohn/SeqPrep) with parameters –q 30 (quality) and –L 35 (minimum merged pair length). Read pairs that did not merge were discarded.