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.

Syllabus

●Access and use of the Galaxy bioinformatics analysis platform

●Quality control and filtering of next-generation sequencing data

●Next-generation sequencing read mapping

●Visualisation of mapped reads with the Integrative Genomics Viewer

●Use of and comparison of software applications to call genomic variants

●Filtering and screening protocols to generate lists of high-confidence SNPs

●Initial annotation of the predicted biological impact of identified variants

Learning Objectives

●Perform QC evaluation and filtering on next-generation sequencing data

●Select and use relevant variant detection software and apply appropriate quality filters to screen variants

●View variant and sequence data using the Integrative Genomics Viewer (IGV)

●Carry out preliminary functional annotation of predicted variants

About Research & analysis

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