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The raw reads were aligned to the human reference genome using default parameters in Bowtie (ver. 1.0.0) (Langmead et al. 2009). The aligned reads were subsequently filtered for quality and uniquely mappable reads using SAMtools (version 0.1.19) (Li et al. 2009) and Picard (version 1.127; http://broadinstitute.github.io/picard/). Relaxed peaks were called using MACS (v2.1.0) (Feng et al. 2012) with a P-value = 1 × 10−2. Additional details about quality control and trimming, read alignment, and peak calling are provided in the Supplemental Methods.
Copyright and License information: ©2018
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
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