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Introduction to RNA-Seq Using Galaxy: Studying the transcriptome

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Audience

The intended audience includes any student, postdoc or RA who has an interest in bioinformatics and who intends to conduct RNA-Seq analysis on a Galaxy platform.

Overview

RNA-Seq is an immensely powerful technique that allows us to examine the presence and quantity of RNA in biological samples. This provides insight into when and where transcription takes place. Processing NGS (next generation sequencing) data is a complex and resource intensive process, involving a number of different software packages and file formats. This course will provide an introduction to those tools on a Galaxy Platform.

Learning outcomes

  • Logging into the Galaxy Server.
  • Accessing Data in Galaxy.
  • Aligning mRNA-seq reads with TopHat
  • Visualising alignments in the Integrated Genome Viewer.
  • Looking for differentially expressed genes with Cufflinks/Cuffdiff
  • A de novo transcriptome assembly using Trinity
  • Finding coding region in a Trinity assembly using TransDecoder

Licence: Other (Not Open)

Keywords: John Innes Centre, JIC

Target audience: Students, postdocs or RAs who have an interest in bioinformatics and who intend to conduct RNA-Seq analysis on a Galaxy platform

Authors: Anmol J. Hemrom

Scientific topics: RNA, RNA-Seq

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