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READemption – A tool for the computational analysis of deep-sequencing-based transcriptome data

View ORCID ProfileKonrad U. Förstner, View ORCID ProfileJörg Vogel, View ORCID ProfileCynthia M. Sharma
doi: https://doi.org/10.1101/003723
Konrad U. Förstner
1Institute for Molecular Infection Biology, University of Würzburg, Würzburg
2Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg
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Jörg Vogel
1Institute for Molecular Infection Biology, University of Würzburg, Würzburg
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Cynthia M. Sharma
2Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg
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ABSTRACT

Summary RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. In order to draw biological conclusions based on RNA-Seq data, several steps some of which are computationally intensive, have to be taken. Our READemption pipeline takes care of these individual tasks and integrates them into an easy-to-use tool with a command line interface. To leverage the full power of modern computers, most subcommands of READemption offer parallel data processing. While READemption was mainly developed for the analysis of bacterial primary transcriptomes, we have successfully applied it to analyze RNA-Seq reads from other sample types, including whole transcriptomes, RNA immunoprecipitated with proteins, not only from bacteria, but also from eukaryotes and archaea.

Availability and Implementation READemption is implemented in Python and is published under the ISC open source license. The tool and documentation is hosted at http://pythonhosted.org/READemption (DOI:10.6084/m9.figshare.977849).

Contact cynthia.sharma{at}uni-wuerzburg.de; konrad.foerstner{at}uni-wuerzburg.de

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 19, 2014.
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READemption – A tool for the computational analysis of deep-sequencing-based transcriptome data
Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma
bioRxiv 003723; doi: https://doi.org/10.1101/003723
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READemption – A tool for the computational analysis of deep-sequencing-based transcriptome data
Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma
bioRxiv 003723; doi: https://doi.org/10.1101/003723

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