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PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data

Summary: 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...

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Detalles Bibliográficos
Autores principales: McCarthy, Michael T., O’Callaghan, Christopher A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998130/
https://www.ncbi.nlm.nih.gov/pubmed/24407222
http://dx.doi.org/10.1093/bioinformatics/btt774
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author McCarthy, Michael T.
O’Callaghan, Christopher A.
author_facet McCarthy, Michael T.
O’Callaghan, Christopher A.
author_sort McCarthy, Michael T.
collection PubMed
description Summary: 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. Availability and implementation: PeaKDEck is written in standard Perl and runs on any platform with Perl installed. PeaKDEck is also available as a standalone application written in Perl/Tk, which does not require Perl to be installed. Files, including a user guide, can be downloaded at: www.ccmp.ox.ac.uk/peakdeck. Contact: chris.ocallaghan@ndm.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-39981302014-04-24 PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data McCarthy, Michael T. O’Callaghan, Christopher A. Bioinformatics Applications Notes Summary: 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. Availability and implementation: PeaKDEck is written in standard Perl and runs on any platform with Perl installed. PeaKDEck is also available as a standalone application written in Perl/Tk, which does not require Perl to be installed. Files, including a user guide, can be downloaded at: www.ccmp.ox.ac.uk/peakdeck. Contact: chris.ocallaghan@ndm.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2014-05-01 2014-01-08 /pmc/articles/PMC3998130/ /pubmed/24407222 http://dx.doi.org/10.1093/bioinformatics/btt774 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
McCarthy, Michael T.
O’Callaghan, Christopher A.
PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
title PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
title_full PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
title_fullStr PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
title_full_unstemmed PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
title_short PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
title_sort peakdeck: a kernel density estimator-based peak calling program for dnasei-seq data
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998130/
https://www.ncbi.nlm.nih.gov/pubmed/24407222
http://dx.doi.org/10.1093/bioinformatics/btt774
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