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RNA-seq data analysis with Chipster
Date: 10.11.2015 9:30 - 10.11.2015 16:30
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: Teaching is provided by Eija Korpelainen and Maria Lehtivaara (CSC)
  • 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
General content: Practical matters:
This hands-on course introduces the participants to RNA-seq data analysis concepts and tools. It covers the whole workflow from quality control (FastQC and PRINSEQ) and alignment (TopHat) to quantification (HTSeq) and differential expression analysis (edgeR and DESeq2), as well as genome browser visualization. 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. Teaching is provided by Eija Korpelainen and Maria Lehtivaara, CSC.
Monday, November 9th

1. How to operate the Chipster software

2. The central steps in RNA-seq data analysis: how to 

  • check the quality of the reads
  • remove bad quality data
  • align RNA-seq reads to the reference genome
  • visualize aligned reads in genomic context
  • count reads per genes
  • check the experiment level quality
  • perform differential expression analysis

3. How to design experiments