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Bioweek: Introduction to RNA-seq data analysis
Date: 06.02.2020 9:00 - 07.02.2020 17:00
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: Maria Lehtivaara
Laxmana Yetukuri
  • free-price-finnish-academics.
  • free-price-others.
All materials, lunches as well as morning and afternoon coffees are free of charge.

If you have registered to this course and you are not able to attend, please cancel your registration in advance by sending an e-mail to
Additional Information
This course is part of the PRACE Training activity. Please visit the PRACE Training portal for further information about the course. For content please contact , for practicalities


After learning the basics of command line usage, HPC and R/Rstudio, it's time to put your new skills in use and use them in RNA-seq data analysis! This course is aimed at bioscientists who are planning on analysing their RNA-seq data. During the course, we will learn the basic steps in RNA-seq analysis and how to use some of the most common analysis tools on command line and in R.

This course is part of the Bioweek 2020. You can participate in ALL or only SELECTED Bioweek's courses. We have planned the Bioweek 2020 so that we are building on top of the previous knowledge. For example, the last course (basics of RNA-seq data analysis) has command line, R/RStudio and CSC services usage as prerequisites. 

Learning outcome

After the course, participants:

  • can name and discuss the different stages of a basic RNA-seq analysis and common tools used in these steps, 
  • can run some RNA-seq analysis tools on command line
  • import and start analysing their RNA-seq data in R


The participants are required to have basic skills/knowledge in:

Bioweek is structured so that this course builds on top of the earlier courses. This means that all the prerequisite skills can be learned on the two courses organised earlier on the same week. If you have no prior knowledge or suspect your knowledge on these subjects, please consider participating in all the three courses. 


Thursday 6.2.

9:00 First session: Welcome & Introductions

  • Welcome & practicalities
  • Intro to RNA-seq  
  • Intro to RNAseq differential expression analysis

10:00 Coffee break
10:30 Second session: Quality control and preprocessing

  • Schedule, materials and pipeline for the course
  • Quality control of raw reads (FASTQC, PRINSEQ)
  • Preprocessing (Trimmomatic)

12:00 Lunch
13:00 Third session: Alignment

  • Indexes for alignment
  • Alignment to reference genome (HISAT2)
  • Check the strandedness (RseQC
  • Alignment level quality control 

14:30 Coffee break
15:00 Fourth session: Quantitation, Experimental design, wrap up for the day

  • Quantitation (HTSEq) 
  • Some notes on experimental design
  • Wrap up of the day 

Friday 7.2.

9:00 First session: Differential expression analysis in R

  • Tiny recap of R
  • Differential expression analysis (edgeR and DESeq2, in R)
  • Experiment level quality control (DESeq2, in R)

10:00 Coffee break
10:30 Second session: Annotations and enrichment analysis

  • Annotations (biomaRt, in R)
  • Enrichment analysis (enrichR, fgsea, in R)

12:00 Lunch
13:00 Third session: Analysing in Puhti + Allas

  • Tiny recap of Puhti 
  • Batch script
  • Allas usage

14:30 Coffee break
15:00 Fourth session: Other topics + wrap up




Course materials