RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

Andrew S Warren; Cristina Aurrecoechea; Brian Brunk; Prerak Desai; Scott Emrich; Gloria I Giraldo-Calderón; 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

doi:10.1093/bioinformatics/btv002

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

Bioinformatics. 2015 May 1;31(9):1496-8. doi: 10.1093/bioinformatics/btv002. Epub 2015 Jan 7.

Authors

Andrew S Warren¹, Cristina Aurrecoechea¹, Brian Brunk², Prerak Desai¹, Scott Emrich², Gloria I Giraldo-Calderón¹, Omar Harb², Deborah Hix¹, Daniel Lawson¹, Dustin Machi¹, Chunhong Mao¹, Michael McClelland¹, Eric Nordberg¹, Maulik Shukla¹, Leslie B Vosshall¹, Alice R Wattam¹, Rebecca Will¹, Hyun Seung Yoo¹, Bruno Sobral¹

Affiliations

¹ Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA, Penn Center for Bioinformatics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46656-0369, USA, University of California, Department of Microbiology and Molecular Genetics, Irvine, California, USA and The Rockefeller University, Howard Hughes Medical Institute, New York, NY 10065, USA.
² Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA, Penn Center for Bioinformatics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46656-0369, USA, University of California, Department of Microbiology and Molecular Genetics, Irvine, California, USA and The Rockefeller University, Howard Hughes Medical Institute, New York, NY 10065, USA Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA, Penn Center for Bioinformatics and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA, Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46656-0369, USA, University of California, Department of Microbiology and Molecular Genetics, Irvine, California, USA and The Rockefeller University, Howard Hughes Medical Institute, New York, NY 10065, USA.

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.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
Bacteria / genetics
Disease Vectors
Gene Expression Profiling / methods*
Genomics
High-Throughput Screening Assays / methods*
Parasites / genetics
Sequence Analysis, RNA / methods*
Software*

Grants and funding

HHSN272200900040C/PHS HHS/United States