ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

ABSTRACT: BACKGROUND: Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results. RESULTS: Here we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration. We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. We also compare ReQON to other available recalibration tools and show that ReQON is less biased and performs favorably in terms of quality score accuracy. CONCLUSION: ReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. ReQON produces a new BAM file with more accurate quality scores, which can improve the results of downstream analysis, and produces several diagnostic plots showing the effectiveness of the recalibration.     

Magnetic fields after translation in Escherichia coli

Quantitative two-dimensional gel electrophoresis of proteins in E. coli exposed for 60 min to weak, pulsed magnetic fields (1.5 mT peak) show that numerous proteins are both increased and decreased by a factor of 2 or more. An increase in the levels of two proteins, the a subunit of DNA-dependent RNA polymerase and NusA, was confirmed by Western blot analysis. © 1994 Wiley-Liss, Inc.     

Ischemia reperfusion dysfunction changes model-estimated kinetics of myofilament interaction due to inotropic drugs in isolated hearts

Background  

The phase-space relationship between simultaneously measured myoplasmic [Ca²⁺] and isovolumetric left ventricular pressure (LVP) in guinea pig intact hearts is altered by ischemic and inotropic interventions. Our objective was to mathematically model this phase-space relationship between [Ca²⁺] and LVP with a focus on the changes in cross-bridge kinetics and myofilament Ca²⁺ sensitivity responsible for alterations in Ca²⁺-contraction coupling due to inotropic drugs in the presence and absence of ischemia reperfusion (IR) injury.