title: Mango: a bias-correcting ChIA-PET analysis pipeline.
abstract: BACKGROUND
  Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity.
  
  
  RESULTS
  Comparison to the existing software packages, ChIA-PET Tool and ChiaSig revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly, Mango executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of the required steps. Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery of known trends in chromatin loops including enrichment of CTCF, RAD21, SMC3 and ZNF143 at the anchor regions of interactions and strong bias for convergent CTCF motifs.
  
  
  METHODS
  Mango is open source and distributed through github at https://github.com/dphansti/mango.
  
  
  BACKGROUND
  mpsnyder@standford.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 and.
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Phanstiel
authors.affiliation: Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Alan P
authors.initials: AP
authors.lastname: Boyle
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 and.
authors.forename: Nastaran
authors.initials: N
authors.lastname: Heidari
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 and.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Snyder
mesh_terms: D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D006801:Humans; D020014:K562 Cells; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013223:Statistics as Topic
chemical_list: D002843:Chromatin