Computational analysis of bacterial RNA-Seq data
By R. Mcclure, D. Balasubramanian, Yan Sun, Maksym Bobrovskyy, P. Sumby, C. Genco, Carin K. Vanderpool, Brian Tjaden. Nucleic Acids Research, 2013
585 citations recorded by the source corpus.
Recent advances in high-throughput RNA sequencing (RNA-seq) have enabled tremendous leaps forward in our understanding of bacterial transcriptomes. However, computational methods for analysis of bacterial transcriptome data have not kept pace with the large and growing data sets generated by RNA-seq technology. Here, we present new algorithms, specific to bacterial gene structures and transcriptomes, for analysis of RNA-seq data. The algorithms are implemented in an open source software system called Rockhopper that supports various stages of bacterial RNA-seq data analysis, including aligning sequencing reads to a genome, constructing transcriptome maps, quantifying transcript abundance, testing for differential gene expression, determining operon structures and visualizing results. We demonstrate the performance of Rockhopper using 2.1 billion sequenced reads from 75 RNA-seq experiments conducted with Escherichia coli, Neisseria gonorrhoeae, Salmonella enterica, Streptococcus pyogenes and Xenorhabdus nematophila. We find that the transcriptome maps generated by our algorithms are highly accurate when compared with focused experimental data from E. coli and N. gonorrhoeae, and we validate our system’s ability to identify novel small RNAs, operons and transcription start sites. Our results suggest that Rockhopper can be used for efficient and accurate analysis of bacterial RNA-seq data, and that it can aid with elucidation of bacterial transcriptomes.
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/326df64f360a722c24b08f02c8d78a1121a4d1f9
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Ecology
In Molecular Biology
Citations in the corpus
- Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center (2016, methodology): “The new service, which can analyze sets of single or paired-end reads, allows users to choose between two workflows for processing RNA-Seq data: Rockhopper (31) or Tuxedo (32).”
- De novo assembly of bacterial transcriptomes from RNA-seq data (2015, background): “In an attempt to address the paucity of computational methods for assembling bacterial transcriptomes from RNA-seq data, we previously developed Rockhopper [12], a system that supports reference-based assembly of bacterial transcriptomes.”