Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus

Background: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional pr...

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Detalles Bibliográficos
Autores: Hansen, Peter, Hecht, Jochen, Ibn-Salem, Jonas, Menkuec, Benjamin S., Roskosch, Sebastian, Truss, Matthias, Robinson, Peter N.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/27873
Acceso en línea:http://hdl.handle.net/10230/27873
http://dx.doi.org/10.1186/s12864-016-3164-6
Access Level:acceso abierto
Palabra clave:Chromatin immunoprecipitation
ChIP-nexus
ChIP-exo
Duplication rates
Library complexity
Algorithm
Bioinformatics
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spelling Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexusHansen, PeterHecht, JochenIbn-Salem, JonasMenkuec, Benjamin S.Roskosch, SebastianTruss, MatthiasRobinson, Peter N.Chromatin immunoprecipitationChIP-nexusChIP-exoDuplication ratesLibrary complexityAlgorithmBioinformaticsBackground: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Results: Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data. Conclusions: The Q-nexus software is efficient and easy to use. Novel statistics about duplication rates in consideration of random barcodes are calculated. Our method for the estimation of the width of the protected region yields unbiased signatures that are highly reproducible for biological replicates and at the same time very specific for the respective factors analyzed. As judged by the irreproducible discovery rate (IDR), our peak calling algorithm shows a substantially better reproducibility. An implementation of Q-nexus is available at http://charite.github.io/Q/.This project was supported by the Bundesministerium für Bildung und Forschung (BMBF; project no. 0313911 and 13GW0099) and the European Community’s Seventh Framework Programme (grant agreement no. 602300; SYBIL). Furthermore, we acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’.BioMed Central201720172016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/27873http://dx.doi.org/10.1186/s12864-016-3164-6reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésBMC Genomics. 2016;17:873info:eu-repo/grantAgreement/EC/FP7/602300© The Author(s). 2016. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to theCreative Commons license, and indicate if changes were made.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/278732026-05-29T05:05:01Z
dc.title.none.fl_str_mv Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
title Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
spellingShingle Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
Hansen, Peter
Chromatin immunoprecipitation
ChIP-nexus
ChIP-exo
Duplication rates
Library complexity
Algorithm
Bioinformatics
title_short Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
title_full Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
title_fullStr Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
title_full_unstemmed Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
title_sort Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus
dc.creator.none.fl_str_mv Hansen, Peter
Hecht, Jochen
Ibn-Salem, Jonas
Menkuec, Benjamin S.
Roskosch, Sebastian
Truss, Matthias
Robinson, Peter N.
author Hansen, Peter
author_facet Hansen, Peter
Hecht, Jochen
Ibn-Salem, Jonas
Menkuec, Benjamin S.
Roskosch, Sebastian
Truss, Matthias
Robinson, Peter N.
author_role author
author2 Hecht, Jochen
Ibn-Salem, Jonas
Menkuec, Benjamin S.
Roskosch, Sebastian
Truss, Matthias
Robinson, Peter N.
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Chromatin immunoprecipitation
ChIP-nexus
ChIP-exo
Duplication rates
Library complexity
Algorithm
Bioinformatics
topic Chromatin immunoprecipitation
ChIP-nexus
ChIP-exo
Duplication rates
Library complexity
Algorithm
Bioinformatics
description Background: ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Results: Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data. Conclusions: The Q-nexus software is efficient and easy to use. Novel statistics about duplication rates in consideration of random barcodes are calculated. Our method for the estimation of the width of the protected region yields unbiased signatures that are highly reproducible for biological replicates and at the same time very specific for the respective factors analyzed. As judged by the irreproducible discovery rate (IDR), our peak calling algorithm shows a substantially better reproducibility. An implementation of Q-nexus is available at http://charite.github.io/Q/.
publishDate 2016
dc.date.none.fl_str_mv 2016
2017
2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/27873
http://dx.doi.org/10.1186/s12864-016-3164-6
url http://hdl.handle.net/10230/27873
http://dx.doi.org/10.1186/s12864-016-3164-6
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv BMC Genomics. 2016;17:873
info:eu-repo/grantAgreement/EC/FP7/602300
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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