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ReadXplorer 2—detailed read mapping analysis and visualization from one single source

Motivation: The vast amount of already available and currently generated read mapping data requires comprehensive visualization, and should benefit from bioinformatics tools offering a wide spectrum of analysis functionality from just one source. Appropriate handling of multiple mapped reads during...

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Autores principales: Hilker, Rolf, Stadermann, Kai Bernd, Schwengers, Oliver, Anisiforov, Evgeny, Jaenicke, Sebastian, Weisshaar, Bernd, Zimmermann, Tobias, Goesmann, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167064/
https://www.ncbi.nlm.nih.gov/pubmed/27540267
http://dx.doi.org/10.1093/bioinformatics/btw541
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author Hilker, Rolf
Stadermann, Kai Bernd
Schwengers, Oliver
Anisiforov, Evgeny
Jaenicke, Sebastian
Weisshaar, Bernd
Zimmermann, Tobias
Goesmann, Alexander
author_facet Hilker, Rolf
Stadermann, Kai Bernd
Schwengers, Oliver
Anisiforov, Evgeny
Jaenicke, Sebastian
Weisshaar, Bernd
Zimmermann, Tobias
Goesmann, Alexander
author_sort Hilker, Rolf
collection PubMed
description Motivation: The vast amount of already available and currently generated read mapping data requires comprehensive visualization, and should benefit from bioinformatics tools offering a wide spectrum of analysis functionality from just one source. Appropriate handling of multiple mapped reads during mapping analyses remains an issue that demands improvement. Results: The capabilities of the read mapping analysis and visualization tool ReadXplorer were vastly enhanced. Here, we present an even finer granulated read mapping classification, improving the level of detail for analyses and visualizations. The spectrum of automatic analysis functions has been broadened to include genome rearrangement detection as well as correlation analysis between two mapping data sets. Existing functions were refined and enhanced, namely the computation of differentially expressed genes, the read count and normalization analysis and the transcription start site detection. Additionally, ReadXplorer 2 features a highly improved support for large eukaryotic data sets and a command line version, enabling its integration into workflows. Finally, the new version is now able to display any kind of tabular results from other bioinformatics tools. Availability and Implementation: http://www.readxplorer.org Contact: readxplorer@computational.bio.uni-giessen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-51670642016-12-20 ReadXplorer 2—detailed read mapping analysis and visualization from one single source Hilker, Rolf Stadermann, Kai Bernd Schwengers, Oliver Anisiforov, Evgeny Jaenicke, Sebastian Weisshaar, Bernd Zimmermann, Tobias Goesmann, Alexander Bioinformatics Original Papers Motivation: The vast amount of already available and currently generated read mapping data requires comprehensive visualization, and should benefit from bioinformatics tools offering a wide spectrum of analysis functionality from just one source. Appropriate handling of multiple mapped reads during mapping analyses remains an issue that demands improvement. Results: The capabilities of the read mapping analysis and visualization tool ReadXplorer were vastly enhanced. Here, we present an even finer granulated read mapping classification, improving the level of detail for analyses and visualizations. The spectrum of automatic analysis functions has been broadened to include genome rearrangement detection as well as correlation analysis between two mapping data sets. Existing functions were refined and enhanced, namely the computation of differentially expressed genes, the read count and normalization analysis and the transcription start site detection. Additionally, ReadXplorer 2 features a highly improved support for large eukaryotic data sets and a command line version, enabling its integration into workflows. Finally, the new version is now able to display any kind of tabular results from other bioinformatics tools. Availability and Implementation: http://www.readxplorer.org Contact: readxplorer@computational.bio.uni-giessen.de Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2016-12-15 2016-08-18 /pmc/articles/PMC5167064/ /pubmed/27540267 http://dx.doi.org/10.1093/bioinformatics/btw541 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Original Papers
Hilker, Rolf
Stadermann, Kai Bernd
Schwengers, Oliver
Anisiforov, Evgeny
Jaenicke, Sebastian
Weisshaar, Bernd
Zimmermann, Tobias
Goesmann, Alexander
ReadXplorer 2—detailed read mapping analysis and visualization from one single source
title ReadXplorer 2—detailed read mapping analysis and visualization from one single source
title_full ReadXplorer 2—detailed read mapping analysis and visualization from one single source
title_fullStr ReadXplorer 2—detailed read mapping analysis and visualization from one single source
title_full_unstemmed ReadXplorer 2—detailed read mapping analysis and visualization from one single source
title_short ReadXplorer 2—detailed read mapping analysis and visualization from one single source
title_sort readxplorer 2—detailed read mapping analysis and visualization from one single source
topic Original Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167064/
https://www.ncbi.nlm.nih.gov/pubmed/27540267
http://dx.doi.org/10.1093/bioinformatics/btw541
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