Journal
BIOINFORMATICS
Volume 30, Issue 23, Pages 3421-3423Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu533
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Funding
- Bavarian Research Network for Molecular Biosystems (BioSysNet)
- BMBF eBio grant RNAsys
- DFG project [VO 875/4-2, Sh580/1-1]
- ZINF Young Investigator program at the Research Center for Infectious Diseases (ZINF, Wurzburg, Germany)
- Young Academy program of the Bavarian Academy of Sciences
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RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. 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 and RNA immunoprecipitated with proteins, not only from bacteria but also from eukaryotes and archaea.
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