================================================================== Uniform Peak calls for Roadmap data from Standardized Epigenomes ================================================================== --------------- Histone mark --------------- For histone marks, narrow peaks were called using MACSv2 (comparing ChIP to corresponding input-DNA control) with a p-value threshold of 0.01. The peaks are not optimally thresholded using IDR. So think of these as a relaxed set of peaks. A user can threshold the peaks using their desired level of stringency. For the broad marks such as H3K36me3, H3K9me3 and H3K27me3, the parameters are not optimal to call broad domains. These peaks represent narrow regions of strong enrichment.. The narrowPeak format is specified here http://genome.ucsc.edu/FAQ/FAQformat.html#format12 ---------------- DNase data --------------- DNase data were processed using two parallel pipelines. (1) *DNase*.macs2.narrowPeak.gz calls were also called using MACS2 with a p-value threshold of 0.01. The narrowPeak format is specified here http://genome.ucsc.edu/FAQ/FAQformat.html#format12 (2) The HotSpot peak caller was also used to call DNase peaks and hotspots (domains). Taken from http://www.uwencode.org/public/rthurman/NREMC/NREMC.html There are 2 files for each DNase dataset: - *DNase*hotspot.all.fdr0.01.pks.bed.gz: narrow Peaks in FDR 1% hotspots (i.e., FDR 1% peaks). 5th column score is peak tag density, 6th column score is z-score. - *DNase*hotspot.all.pks.bed.gz: Genome-wide tag density peak calls. These are not restricted to hotspots, thresholded or unthresholded. Score column is peak tag density