Training and EventsRNA-seq data analysis workshop - Training
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| Date: | 08.01.2014 12:00 - 11.01.2014 16:00 |
| Location details: | - |
| Language: | english-language |
| lecturers: |
Several speakers as indicated in the program. |
| Price: | - |
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.
Tuesday 7.1.2014
Coffee
FULL! 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)
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. The instructions can be found here.
Thursday 9.1.2014
Coffee
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)
- 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)
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14:00-14:50 Joint analysis of miRNA and mRNA expression data (Angel Rubio, CEIT, Spain)
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
Coffee
FULL! 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.
Lunch
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.