RNA-seq data analysis workshop

rna-seqThis international workshop covers several aspects of RNA-seq data analysis, ranging from quality control, assembly and alignment to differential expression analysis and miRNA-mRNA integration. Particular emphasis is given to comparison of different analysis tools.

The program consists of two lecture days and four hands-on sessions. You can register only for the lectures, or select some hands-on tutorials as well. Please note that there can be still slight changes to the schedule, as some additional speakers might be added.

This workshop is kindly sponsored by the FP7 AllBio project, which aims to bring biologists and bioinformaticians together for the effective exploitation of high-throughput data.


Wednesday 8.1.2014

10:00-10:15 Welcome (Eija Korpelainen, CSC)

10:15-12:00 Quality control and alignment

  • Quality checking and pre-processing your RNA-seq data (Mikael Huss, SciLifelab, Sweden)
  • Systematic evaluation of spliced aligners for RNA-seq (Pär Engström, SciLifelab, Sweden)

12:00-13:00 Lunch

13:00-15:00 Reliability of RNA-seq, differential expression analysis

  • Reliability and interpretation of RNA-Seq expression profiles (Pawel Labaj, BOKU, Austria)
  • Transcript isoform expression and differential expression estimation with BitSeq (Antti Honkela, University of Helsinki, Finland)
  • Comparison of differential expression analysis tools (Laura Elo, University of Turku, Finland)
15:00-18:00 Hands-on tutorial 1: Differential expression analysis using R/Bioconductor and Unix (Mikael Huss)
This hands-on session covers quantification and differential expression analysis of RNA-seq data. The analysis tools used in the exercises include command line applications and Bioconductor packages such as Cuffdiff and DESeq2, so participants need to be familiar with Unix and R.

Thursday 9.1.2014

10:00-12:00 Transcriptome assembly

  • Introduction to transcriptome assembly (Panu Somervuo, University of Helsinki, Finland)
  • Targeted assembly of RNA-seq data using phylogenetic information (Ari Löytynoja, University of Helsinki, Finland)
  • TBA

12:00-13:00 Lunch

13:00-15:00 miRNA-seq data analysis

  • Introduction to small RNA sequence analysis with applications in nematodes (Garry Wong, UEF, Finland)
  • Small RNA data analysis and miRNA discovery in plants and mammalians (Andreas Gisel, ITB, Italy)
  • Joint analysis of miRNA and mRNA expression data (Angel Rubio / Ander Muniategui, CEIT, Spain)
15:00-18:00 Hands-on tutorial 2: Small RNA data analysis (Andreas Gisel)
This tutorial covers a command line based workflow to find known and novel miRNAs using tools like BWA and mirDeep2, so participants should be familiar with Unix. The workflow is developed at ITB, Italy, and it reports the results in a graphical form allowing an easy way to extract the required information.

Friday 10.1.2014

9:00-12:00 Hands-on tutorial 3: RNA-seq data analysis using Chipster (Eija Korpelainen)
This tutorial covers quality control (FastQC and PRINSEQ), alignment (TopHat) and quantification (HTSeq) as well as differential expression analysis (edgeR and DESeq) and genome browser visualization. The user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required and the tutorial is thus suitable for everybody.

12:00-13:00 Lunch

13:00-16:00 Hands-on tutorial 4: Using cluster and grid computing in RNA-seq data-analysis (Kimmo Mattila)
This tutorial demonstrates how researchers working in Finland can utilize the cluster capacity of CSC and the FGI grid environment for computationally demanding analysis tasks. In these environments you can run tools like Trinity or TopHat using tens or hundreds of computing cores. The knowledge of Unix is required for this session.
Date: 08.01.2014 10:00 – 10.01.2014 16:00
Location: Premises of CSC at Keilaranta 14, Espoo, Finland. The lectures are organized in the auditorium, while the hands-on tutorials take place in the computer classroom. More information about the location, transport and nearby hotels can be found here. The nearest airport is Helsinki-Vantaa (40 min by taxi from CSC).
Language: English
Lecturers: Several speakers as indicated in the program.

Price: 40 EUR per day, including VAT

The fee covers coffees, lunches and course materials.


Registration form Registration by 12.12.2013 23:00.

NOTE: If you register for the hands-on tutorials, please indicate which group you come from and briefly describe your motivation. Due to space constraints the maximum number of people in the tutorials is 24. If there are more applicants, priority is given to people who need to analyze RNA-seq data soon. We also try to offer a place for at least one person from each research group. All the applicants will be informed about the selection by 16.12.2013. Please remember to cancel your registration if you cannot make it, so that your place can be given to waitlisted people. The registration fee will not be charged if you cancel before 2.1.2014.

Additional information

For additional information, please contact eija.korpelainen[at]csc.fi