ABACBS is delighted to be able to present this workshop in conjunction with the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET).


9am-5pm, Thursday November 10th, 2016


O-Block Room O-508, Queensland University of Technology, 2 George St., Brisbane QLD 4000

Faculty: Dr Eija Korpelainen, CSC-IT Center for Science Ltd, Espoo, Finland

Eija Korpelainen received her PhD from the University of Adelaide in 1996 after working on hemopoietic growth factors and vascular endothelium. She continued the endothelial work as an EMBO postdoctoral fellow in the University of Helsinki, Finland. Gradually moving to bioinformatics, she joined CSC – IT Center for Science in 2001. CSC is the national supercomputing center in Finland. In her role as bioinformatics specialist Dr Korpelainen provides nation-wide bioinformatics services including training, user support and software development and, in particular, has directed the development of Chipster (http://chipster.csc.fi/), biologist-friendly analysis software for sequencing and microarray data. Chipster is free and there are server installations world-wide. In addition to her current position as Chipster product manager, Dr Korpelainen runs data analysis courses in Finland and abroad and participates in several international bioinformatics projects such as ELIXIR. In order to enable researchers to analyse their own data, she and her colleagues wrote the book, RNA-seq data analysis: A practical approach

RNA-seq data analysis with Chipster

This hands-on course introduces the participants to RNA-seq data analysis methods, tools and file formats. It covers the whole workflow from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. 

 You will learn how to:

  • check the quality of reads with FastQC and PRINSEQ
  • remove bad quality data with Trimmomatic
  • align RNA-seq reads to the reference genome with TopHat2
  • visualize aligned reads in genomic context using the Chipster genome browser
  • perform alignment level quality control using RseQC and SAMtools
  • quantify expression by counting reads per genes using HTSeq
  • check the experiment level quality with PCA plots and heatmaps
  • analyze differential expression with DESeq2 and edgeR
  • take multiple factors (including batch effects) into account in differential expression analysis

Who should attend?

This course is suitable to those who intend to employ RNA-seq in their research and who would like to understand the concepts underlying this method, even if they do not intend to analyse the data themselves. 

The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required.

This event is being held in a computer lab which will have the necessary software installed so there is no need to bring a laptop.


Contact annette.mcgrath@csiro.au with any questions.


from 40.00
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