RNA-Rocket @ Pathogen Portal
Supports comparative analysis of host response to pathogens. It provides an RNA-Seq pipeline to characterize the transcriptome of all NIAID Bioinformatic Resource Center (BRC) pathogens and their key hosts.
This is a Domain specific server.
- From Lew, et al.
- "It can analyze transcriptome data for genomes stored at EuPathDB, PATRIC, and VectorBase. The pipeline is built on Galaxy. Galaxy has been modified to simplify RNA-Seq analysis for informatics-naïve, biologically focused users and provide a guided experience to quality control of read data, read mapping, assembling transcripts, estimating gene expression values, and doing differential expression analysis"
- VBI-led Team Introduces Infectious Disease-focused Resource for Analyzing RNA-seq Data, by Andrea Anderson, GenomeWeb, February 3, 2015
- Map your RNA-Seq Reads to Reference Genomes: Align your Illumina fastQ reads (gzipped fastQ files accepted) against any sequenced genome from EuPathDB, PATRIC, and VectorBase.
Estimate Gene Expression Values: Obtain BAM files for the resulting alignments and FPKM expression values for annotated genes and novel transcripts.
- The RNA-Rocket implementation was also covered by Andrew Warren at the May 2013 GalaxyAdmins meetup. A Screencast and the slides are both available.
- Need to create a login
- RNA-Rocket: an RNA-Seq analysis resource for infectious disease research, by Warren et al., Bioinformatics (2015) doi: 10.1093/bioinformatics/btv002
- RNA-Rocket tagged publications in Galaxy Publication library.
- The Pathogen Portal and PATRIC projects have been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272200900040C, awarded to BWS Sobral.