Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering

BMC Bioinformatics

Methodology Article

Mariam Farman¹  Lydia Müller¹  Dirk Zeckzer²  Daniel Gerighausen² 

[1] Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16–18, 04107, Leipzig, Germany;Image and Signal Processing Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, 04109, Leipzig, Germany;

关键词: ChIP-seq;    Peak-caller;    Histone modifications;    Replicate analysis;   

DOI  :  10.1186/s12859-016-1248-6

 received in 2016-04-10, accepted in 2016-09-08,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundHistone 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.ResultsWe 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.ConclusionWe 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.

【 授权许可】

CC BY   
© The Author(s) 2016