title: BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.
abstract: CONCLUSIONS
  Although some histone modification chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) signals show abrupt peaks across narrow and specific genomic locations, others have diffuse distributions along chromosomes, and their large contiguous enrichment landscapes are better modeled as broad peaks. Here, we present BroadPeak, an algorithm for the identification of such broad peaks from diffuse ChIP-seq datasets. We show that BroadPeak is a linear time algorithm that requires only two parameters, and we validate its performance on real and simulated histone modification ChIP-seq datasets. BroadPeak calls peaks that are highly coincident with both the underlying ChIP-seq tag count distributions and relevant biological features, such as the gene bodies of actively transcribed genes, and it shows superior overall recall and precision of known broad peaks from simulated datasets.
  
  
  BACKGROUND
  The source code and documentations are available at http://jordan.biology.gatech.edu/page/software/broadpeak/.
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
authors.forename: Jianrong
authors.initials: J
authors.lastname: Wang
authors.forename: Victoria V
authors.initials: VV
authors.lastname: Lunyak
authors.forename: I King
authors.initials: IK
authors.lastname: Jordan
mesh_terms: D000465:Algorithms; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D006801:Humans; D012984:Software
chemical_list: D006657:Histones