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CSC - IT CENTER FOR SCIENCE Finland
RNA-seq data analysis workshop
8th - 10th January 2014
Helsinki, Finland
Program
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.
Wednesday 8.1.2014
Registration and coffee
10:00 Welcome (Eija Korpelainen, CSC)
Session I: Quality control and alignment
10:15-11:05 Quality checking and pre-processing your RNA-seq data (Mikael Huss, SciLifelab, Sweden)
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
13:00-13:45 Reliability and interpretation of RNA-Seq expression profiles (Pawel Labaj, BOKU, Austria)
13:45-14:20 Transcript isoform expression and differential expression estimation with BitSeq (Antti Honkela, University of Helsinki, Finland)
14:20-15:00 Comparison of differential expression analysis tools (Laura Elo, University of Turku, Finland)
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.
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