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Bioweek: RNA-seq data analysis with Chipster
Date: 06.03.2017 9:00 - 06.03.2017 16:00
Location details: The event is organised at the CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. The best way to reach us is by public transportation; more detailed travel tips are available.
Language: english-language
lecturers: Eija Korpelainen
Maria Lehtivaara
  • 60 for-finnish-academics
  • 280 for-others
The fee covers all materials, lunches as well as morning and afternoon coffees.
The seats are filled in the registration order. You may cancel your attendance without a charge 5 business days prior the course. For cancellations after that and no-shows without a cancellation the full fee will be invoiced.
Additional Information


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

You will learn how to

  • check the quality of reads with FastQC and PRINSEQ
  • remove bad quality data with Trimmomatic
  • infer strandedness with RseQC
  • 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


Target audience: Life scientists who are planning to apply RNA-seq analysis in their research. This course is suitable also for those researchers who do not plan to analyse data themselves, but who need to understand the concepts in order to discuss with bioinformaticians.