James Bond meets Next-generation sequencing: an introduction to RNA-Seq data analysis using the “Tuxedo” Suite pipeline available in the Galaxy web-based platform

RNA-Seq has become increasingly popular in transcriptome profiling and is used primarily to determine differential expression of genes or transcripts as well as identifying novel transcripts. The analysis of RNA-seq data most commonly includes:  quality control, filtering, read alignment, assigning reads to genes or transcripts, and estimating transcript abundance. There is currently a vast number of tools that are currently available and accessible, such as Galaxy, which help simplify the processing and analysis of RNA-Seq data. Galaxy is a user-friendly web-based platform that offers all of the tools necessary for creating and performing a complete intensive RNAseq data analysis workflow or pipeline.

A Galaxy workshop was co-hosted by ACGT and The Genomics Research Institute (GRI) between the 1st and 3rd of July 2015 at the University of Pretoria. This workshop forms part of a series of open-source bioinformatics training workshops planned for 2015 that is being co-sponsored by the Bioinformatics Service Platform (BSP) and the ACGT. The overall aim of this workshop was to provide a hands-on tutorial for different aspects of RNA-Seq analyses, from data preparation, through to statistical testing for differential gene expression. This workshop was specifically designed to teach participants how to integrate data, and perform simple and complex analysis within Galaxy using the “Tuxedo” suite of tools. The Tuxedo suite is specially comprised of Bowtie (alignment), Tophat (mapping) and Cufflinks (transcript abundance).

The first day of the workshop kicked off with a brief welcome and opening remarks by Dr Farhahna Allie (ACGT Support Scientist) and Prof Fourie Joubert. This was followed by a brief “ice-breaker” introduction by the attendees. Each day of the workshop started off with a lecture session in the morning and a hands-on session in the afternoon. In the afternoon session, the attendees had the opportunity to apply what they had learnt in the morning to real data through a variety of exercises. Datasets for the workshop was provided and although the workshop required that attendees have some basic understanding and knowledge of Linux commands and/or R commands, these commands were fully documented and provided to each participant.


Overall, the positive feedback from delegates indicated that the course was presented well and useful. This workshop was particularly successful as it highlighted the expertise of local South African trainers: Prof Fourie Joubert, Dr Charles Hefer and Dr. Oliver Bezuidt.

For more information on upcoming bioinformatics training events, visit the events page on the ACGT website (www.acgt.co.za), like us on Facebook (http://www.facebook.com/ACGT.biotec or contact Farhahna Allie at

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