title: Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering.
abstract: BACKGROUND
  Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed.
  
  
  RESULTS
  We propose a new peak-caller called 'Sierra Platinum' that allows peak-calling of replicated ChIP-seq experiments. Moreover, it provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and the resulting peaks, as well as steering the peak-calling process.
  
  
  CONCLUSIONS
  We show that Sierra Platinum outperforms currently available methods using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project. It is robust against noisy replicates.
authors.affiliation: Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany. lydia@bioinf.uni-leipzig.de.
authors.forename: Lydia
authors.identifier: http://orcid.org/0000-0001-9544-121X
authors.initials: L
authors.lastname: Müller
authors.affiliation: Image and Signal Processing Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, Leipzig, 04109, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Gerighausen
authors.affiliation: Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, Leipzig, 04107, Germany.
authors.forename: Mariam
authors.initials: M
authors.lastname: Farman
authors.affiliation: Image and Signal Processing Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, Leipzig, 04109, Germany.
authors.forename: Dirk
authors.initials: D
authors.lastname: Zeckzer
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods* / Q000592:standards; D057890:Epigenomics; D042421:Histone Code; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards
keywords: ChIP-seq; Histone modifications; Peak-caller; Replicate analysis