CSC - IT CENTER FOR SCIENCE Finland

RNA-seq data analysis workshop

8th - 10th January 2014

Helsinki, Finland

http://www.csc.fi/english/csc/courses/archive/rnaseq2014

Program

Thursday 9.1.2014

Session III: Transcriptome assembly

10:00-10:30 Introduction to transcriptome assembly (Panu Somervuo, University of Helsinki, Finland) 10:30-11:00 Assessment of transcript reconstruction methods for RNA-seq (Pär Engström, SciLifelab, Sweden) 11:00-11:30 Targeted assembly of RNA-seq data using phylogenetic information (Ari Löytynoja, University of Helsinki, Finland) Session IV: miRNA-seq data analysis 11:30-12:20 Introduction to small RNA sequence analysis with applications in nematodes (Garry Wong, UEF, Finland) Lunch

13:20-14:00 Small RNA data analysis and miRNA discovery in plants and mammalians (Andreas Gisel, ITB, Italy) 14:00-14:50 Joint analysis of miRNA and mRNA expression data (Angel Rubio, CEIT, Spain)

Coffee

BOOKED OUT! 15:00-18:00 Hands-on tutorial 2: Small RNA data analysis (Andreas Gisel CNR-ITB) 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.


Wednesday 8.1.2014 Registration and coffee

  1. 10:00 Welcome (Eija Korpelainen, CSC)

Session I: Quality control and alignment

  1. 10:15-11:05 Quality checking and pre-processing your RNA-seq data (Mikael Huss, SciLifelab, Sweden)
  2. 11:05-12:00 Systematic evaluation of spliced aligners for RNA-seq (Pär Engström, SciLifelab, Sweden)

Lunch

Session II: Reliability of RNA-seq, differential expression analysis

  1. 13:00-13:45 Reliability and interpretation of RNA-Seq expression profiles (Pawel Labaj, BOKU, Austria)
  2. 13:45-14:20 Transcript isoform expression and differential expression estimation with BitSeq (Antti Honkela, University of Helsinki, Finland)
  3. 14:20-15:00 Comparison of differential expression analysis tools (Laura Elo, University of Turku, Finland)
  4. Coffee

BOOKED OUT! 15:00-18:00 Hands-on tutorial 1: Differential expression analysis using R/Bioconductor and Unix (Mikael Huss, Pär Engström) 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.  Instructions by the trainers
Tuesday 7.1.2014

Coffee

BOOKED OUT! 12:00-15:00 Additional 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.

This workshop consists of two lecture days and four hands-on sessions. More information and registration can be found here.

Speakers

  • Mikael Huss (SciLifelab, Sweden): Quality checking and pre-processing your RNA-seq data
  • Pawel Labaj (BOKU, Austria): Reliability and interpretation of RNA-Seq expression profiles
  • Pär Engström (SciLifelab, Sweden): Systematic evaluation of spliced aligners for RNA-seq
  • Panu Somervuo (University of Helsinki, Finland): Introduction to transcriptome assembly
  • Ari Löytynoja (University of Helsinki, Finland): Targeted assembly of RNA-seq data using phylogenetic information
  • Laura Elo (University of Turku, Finland): Comparison of differential expression analysis tools
  • Antti Honkela (University of Helsinki, Finland): BitSeq - transcript isoform expression and differential expression estimation from RNA-seq data
  • Garry Wong (UEF, Finland): An introduction to small RNA sequence analysis with applications in nematodes
  • Andreas Gisel (ITB, Italy): smallRNA data analysis and miRNA discovery in plants and mammalians
  • Angel Rubio / Ander Muniategui (CEIT, Spain): Joint analysis of miRNA and mRNA expression data
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