RT Journal Article
SR Electronic
T1 SUPERmerge: ChIP-seq coverage island analysis algorithm for broad histone marks
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 121897
DO 10.1101/121897
A1 Bohdan B. Khomtchouk
A1 Derek Van Booven
A1 Claes Wahlestedt
YR 2017
UL http://biorxiv.org/content/early/2017/03/29/121897.abstract
AB 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