Rif-Correct, a software tool for bacterial mRNA half-life estimation

Abstract

BackgroundGenome-wide measurement of bacterial mRNA lifetimes using the antibiotic rifampicin has provided new insights into the control of bacterial mRNA decay. However, for long polycistronic mRNAs, the estimation of mRNA half-life can be confounded with transcriptional runoff caused by rifampicins inhibition of initiating RNA polymerases, and not elongating RNA polymerases. ResultsWe present the Rif-correct software package, a free open-source tool that uses transcriptome models of transcript architecture to allow for more accurate mRNA half-life estimates that account for the transcriptional runoff. Rif-correct is implemented as a customizable python script that allows for users to control all the analysis parameters to achieve improved mRNA half-life estimates. ConclusionsRif-correct is the first free open-source computational analysis pipeline for Rif-seq dataset mRNA half-life estimation. It is simple to run, fast, and easy to run with a detailed instruction manual and example datasets.