Evaluation of algorithm performance in ChIP-seq peak detection.

Evaluation of algorithm performance in ChIP-seq peak detection.

Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions. Identification of protein binding sites from ChIP-seq data has required novel computational tools, distinct from those used for th...

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Autores principales: Elizabeth G Wilbanks, Marc T Facciotti
Formato: article
Lenguaje:EN
Publicado: Public Library of Science (PLoS) 2010
Materias:
Medicine
R
Science
Q
Acceso en línea:https://doaj.org/article/41a342b9d62a4e089492c53aac29ad69
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spelling oai:doaj.org-article:41a342b9d62a4e089492c53aac29ad692021-12-02T20:20:15ZEvaluation of algorithm performance in ChIP-seq peak detection.1932-620310.1371/journal.pone.0011471https://doaj.org/article/41a342b9d62a4e089492c53aac29ad692010-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20628599/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions. Identification of protein binding sites from ChIP-seq data has required novel computational tools, distinct from those used for the analysis of ChIP-Chip experiments. The growing popularity of ChIP-seq spurred the development of many different analytical programs (at last count, we noted 31 open source methods), each with some purported advantage. Given that the literature is dense and empirical benchmarking challenging, selecting an appropriate method for ChIP-seq analysis has become a daunting task. Herein we compare the performance of eleven different peak calling programs on common empirical, transcription factor datasets and measure their sensitivity, accuracy and usability. Our analysis provides an unbiased critical assessment of available technologies, and should assist researchers in choosing a suitable tool for handling ChIP-seq data.Elizabeth G WilbanksMarc T FacciottiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 7, p e11471 (2010)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Elizabeth G Wilbanks
Marc T Facciotti
Evaluation of algorithm performance in ChIP-seq peak detection.
description Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions. Identification of protein binding sites from ChIP-seq data has required novel computational tools, distinct from those used for the analysis of ChIP-Chip experiments. The growing popularity of ChIP-seq spurred the development of many different analytical programs (at last count, we noted 31 open source methods), each with some purported advantage. Given that the literature is dense and empirical benchmarking challenging, selecting an appropriate method for ChIP-seq analysis has become a daunting task. Herein we compare the performance of eleven different peak calling programs on common empirical, transcription factor datasets and measure their sensitivity, accuracy and usability. Our analysis provides an unbiased critical assessment of available technologies, and should assist researchers in choosing a suitable tool for handling ChIP-seq data.
format article
author Elizabeth G Wilbanks
Marc T Facciotti
author_facet Elizabeth G Wilbanks
Marc T Facciotti
author_sort Elizabeth G Wilbanks
title Evaluation of algorithm performance in ChIP-seq peak detection.
title_short Evaluation of algorithm performance in ChIP-seq peak detection.
title_full Evaluation of algorithm performance in ChIP-seq peak detection.
title_fullStr Evaluation of algorithm performance in ChIP-seq peak detection.
title_full_unstemmed Evaluation of algorithm performance in ChIP-seq peak detection.
title_sort evaluation of algorithm performance in chip-seq peak detection.
publisher Public Library of Science (PLoS)
publishDate 2010
url https://doaj.org/article/41a342b9d62a4e089492c53aac29ad69
work_keys_str_mv AT elizabethgwilbanks evaluationofalgorithmperformanceinchipseqpeakdetection
AT marctfacciotti evaluationofalgorithmperformanceinchipseqpeakdetection
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