TY - JOUR T1 - SUPERmerge: ChIP-seq coverage island analysis algorithm for broad histone marks JF - bioRxiv DO - 10.1101/121897 SP - 121897 AU - Bohdan B. Khomtchouk AU - Derek Van Booven AU - Claes Wahlestedt Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/03/29/121897.abstract N2 - SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. SUPERmerge is especially useful for investigating low sample size ChIP-seq experiments in which epigenetic histone modifications (e.g., H3K9me1, H3K27me3) result in inherently broad peaks with a diffuse range of signal enrichment spanning multiple consecutive genomic loci and annotated features.bpbase pairsChIP-seqchromatin immunoprecipitation followed by massively parallel DNA sequencingIDRirreproducible discovery rateQCquality controlTFtranscription factor ER -