Chunk #53 — Online Methods — 1. Data matrix, primary analysis and processing, quality control — 1.2 ChIP-seq and DNase-seq uniform reprocessing for consolidated epigenomes — c. Peak Calling
For DNase-seq data, we used two methods to identify DNaseI-accessible sites. First, the Hotspot algorithm was used to identify fixed-size (150bp) DNase hypersensitive sites, and more general-sized regions of DNA accessibility (hotspots) using an FDR of 0.01 (http://www.uwencode.org/proj/hotspot)103. MACSv2.0.10 was also used to call narrow peaks using the same settings specified above for the histone mark narrow peak calling.
