Introduction

Hypersensitivity to DNaseI digestion is a hallmark of open chromatin, and DNaseI-seq allows the genome-wide identification of regions of open chromatin. Interpreting these data is challenging, largely because of inherent variation in signal-to-noise ratio between datasets. We have developed PeaKDEck, a peak calling program that distinguishes signal from noise by randomly sampling read densities and using kernel density estimation to generate a dataset-specific probability distribution of random background signal. PeaKDEck uses this probability distribution to select an appropriate read density threshold for peak calling in each dataset. We benchmark PeaKDEck using published ENCODE DNaseI-seq data and other peak calling programs, and demonstrate superior performance in low signal-to-noise ratio datasets.

Publications

  1. PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data.
    Cite this
    McCarthy MT, O'Callaghan CA, 2014-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Michael T McCarthy
    Developer

    Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine

  2. Christopher A O'Callaghan
    Investigator

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Summary
AccessionBT001212
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByChristopher A O'Callaghan