Introduction

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.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.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.

Publications

  1. Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering.
    Cite this
    Müller L, Gerighausen D, Farman M, Zeckzer D, 2016-09-01 - BMC bioinformatics

Credits

  1. Lydia Müller
    Developer

    Bioinformatics Group, Department of Computer Science, Germany

  2. Daniel Gerighausen
    Developer

    Image and Signal Processing Group, Department of Computer Science, Germany

  3. Mariam Farman
    Developer

    Bioinformatics Group, Department of Computer Science, Germany

  4. Dirk Zeckzer
    Investigator

    Image and Signal Processing Group, Department of Computer Science, Germany

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006796
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByDirk Zeckzer