RNA-Rocket @ Pathogen Portal

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Summary: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.

Comments

  • 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-na├»ve, 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"
  • 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.

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