(Workshop formerly known as RNA-Seq using Galaxy.)

This is a QFAB course and places are highly limited as Graduate School is paying the fee. If you are unable to attend, please de-register (or email graduateschool@uq.edu.au if you are unable to do so). An unexplained absence could result in all your future QFAB registrations becoming Waitlisted.

The workshop will start with an introduction to the tools and workflows of RNA-Seq analysis using the Galaxy bioinformatics platform before moving onto R for more advanced differential gene expression analysis. Practical exercises will include quality control and normalisation of data, differential gene expression analysis, and linking of data to external resources for more in depth interpretation. The workshop is recommended for biologists and bioinformaticians wishing to use R for RNA expression analysis.

Learning Objectives

  • Reading and Parsing FastQ files
  • Carry out standard QC tests on RNA-Seq datasets
  • Use the limma-voom R package to produce lists of differentially expressed genes
  • Use of Biomart for annotation of transcripts
  • Use of GoStats to perform enrichment analysis

Syllabus

  • Pre-processing and quality control of RNA-Seq data
  • Mapping and quantification of read data
  • Identification of differentially-expressed genes
  • Annotation of transcripts
  • Systems biology interpretation of gene lists using pathway enrichment analysis

About Research & analysis

Stand a change to win a $20 Student Union voucher! Find the navigation of Research & Analysis confusing? Take part in our fun card sort survey to help us classify the courses in a manner that makes most sense to you! Survey closes 22 November 2019, noon.

Your research degree requires the ability to apply …'analytical and critical thinking skills to generate new knowledge, investigate problems and develop inventive solutions.' (UQ HDR Graduate Attributes, 2017) This starts with the way you design your project, your review of existing literature, the methodologies you use and the analysis you apply. Building these skills during your research degree will equip you to engage these same skills in your future career and apply them in a wide variety of contexts. 

Research methods

The Graduate School has a range of research methods sessions available.

Qualitative Research Institute for Social Science Research (ISSR) Queensland Facility for Advanced Bioinformatics (QFAB)

Library workshops

The library offers a range of workshops under the headings below. 

R and Python Research data management Data visualisation

Useful links

  • RStudio cheat sheets
  • Data Management at UQ (UQRDM) 
  • Sage Research Methods 
  • Join Sage’s Methodspace 
  • Publons Academy: A free online course for peer reviewers
  • Hacky Hour (supported by RCC, QCIF, IMB and wonderful volunteer helpers!): RCC runs consultations every Tuesday at Cafe Nano. Come and ask IT questions such as: getting started with Python and R, stats, machine learning, bio-image, software tools, research data management (RDM), how to access high performance computing, cloud data storage and tools for data cleaning and data visualisation. Bring your project's IT problems or come along as a helper! Very occasionally Hacky Hour may not run; follow us on Twitter (@HackyHourStLuc​) to get the latest announcements. Aside from the usual IT research questions, 
    • First Tuesday of the monthBioinformatics Hacky Hour, ask bioinformatics analysis, software and pipeline questions
    • Last Tuesday of the monthBioLab Hacky Hour, ask about experimental design and technical sample processing questions to get started in the lab