Published December 7, 2014
| Version v1
Software
Open
Data analysis scripts for the transcriptional start site detection of Vibrio cholerae O1
Creators
- 1. Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- 2. Research Centre for Infection Diseases (ZINF), University of Würzburg, D-97080, Germany
Description
These Shell and Python scripts accompany the manuscript "Differential RNA-seq analysis of Vibrio cholerae identifies the VqmR sRNA as a regulator of collective behaviors" by Kai Papenfort, Konrad U. Förstner, Jian-Ping Cong, Cynthia M. Sharma and Bonnie L. Bassler (doi:10.1073/pnas.1500203112).
The script "run_analysis.sh" performs the retrieval of the required data, the RNA-Seq data analysis using READemption as well as the Transcriptional start site (TSS) prediction using TSSpredator. As several tools are required to run the analysis the script "install_software.sh" assists with installing those programs. It might need to be adjusted to the system on which the analysis will be performed.
Files
Files
(30.7 kB)
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md5:1b22c9039d2d2af2955304fab3ab103b
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Additional details
Related works
- Is supplement to
- 10.1073/pnas.1500203112 (DOI)
- PMID:25646441 (PMID)
- PMC4343088 (pmcid)
References
- Papenfort K, Förstner KU, Cong JP, Sharma CM, Bassler BL. Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm
- formation. Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):E766-75. doi:10.1073/pnas.1500203112. Epub 2015 Feb 2. PubMed PMID: 25646441; PubMed Central
- PMCID: PMC4343088. http://www.pnas.org/content/112/7/E766.abstract