RNA-Rocket: an RNA-Seq Analysis Resource for Infectious Disease Research

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2015 Jan 10

PMID 25573919

Citations 5

Authors

Andrew S Warren

Cristina Aurrecoechea

Brian Brunk

Prerak Desai

Scott Emrich

Gloria I Giraldo-Calderon

Omar Harb

Deborah Hix

Daniel Lawson

Dustin Machi

Chunhong Mao

Michael McClelland

Eric Nordberg

Maulik Shukla

Leslie B Vosshall

Alice R Wattam

Rebecca Will

Hyun Seung Yoo

Bruno Sobral

Affiliations

Soon will be listed here.

Abstract

Motivation: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers.

Results: RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data.

Availability And Implementation: RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal.

Contact: anwarren@vt.edu

Supplementary Information: Supplementary materials are available at Bioinformatics online.

Citing Articles

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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.

Wattam A, Davis J, Assaf R, Boisvert S, Brettin T, Bun C Nucleic Acids Res. 2016; 45(D1):D535-D542.

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