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Over one and a half days participants will be given a hands-on introduction to RNA-seq data analysis: from raw sequence reads to differentially expressed genes – introducing the theory, analysis tools and file formats involved. The program consists of alternating short lectures and hands-on exercises.
Participants will learn and practise how to:
•check the quality of reads with FastQC and PRINSEQ
•remove bad quality data with Trimmomatic
•align RNA-seq reads to the reference genome with TopHat2
•visualise aligned reads in genomic context using the Chipster genome browser
•perform alignment level quality control using RseQC and SAMtools
•quantify expression by counting reads per genes using HTSeq
•check the experiment level quality with PCA plots and heatmaps
•analyse differential expression with DESeq2 and edgeR
•take multiple factors (including batch effects) into account in differential expression analysis.
Who should attend?
Life scientists who are planning to apply RNA-seq analysis in their research. This course is suitable also for those researchers who do not plan to analyse data themselves, but who need to understand the concepts in order to discuss with bioinformaticians. The opportunity to see how Eija leads this workshop will also be valuable for those who teach RNA-Seq concepts to scientists.
Dr Eija Korpelainen, CSC-IT Center for Science Ltd, Espoo, Finland
Eija Korpelainen received her PhD from the University of Adelaide in 1996 after working on hemopoietic growth factors and vascular endothelium. She continued the endothelial work as an EMBO postdoctoral fellow in the University of Helsinki, Finland. Gradually moving to bioinformatics, she joined CSC – IT Center for Science in 2001. CSC is the national supercomputing center in Finland. In her role as bioinformatics specialist Dr Korpelainen provides nation-wide bioinformatics services including training, user support and software development and, in particular, has directed the development of Chipster (http://chipster.csc.fi/), biologist-friendly analysis software for sequencing and microarray data. Chipster is open source and there are server installations world-wide. In addition to her current position as Chipster product manager, Dr Korpelainen runs data analysis courses in Finland and abroad and participates in several international bioinformatics projects such as ELIXIR. In order to enable researchers to analyse their own data, she and her colleagues wrote the book, RNA-seq data analysis: A practical approach.
We are pleased to offer this workshop in conjunction with GOBLET, the Global Organisation for Bioinformatics Learning, Education & Training. Hosted at EMBL-ABR: VLSCI Node.
$45 - instructions on making the online payment (outside of the Eventbrite system) will be provided after registraton. This workshop is fully catered.
Please bring your laptop. Instructions on setup and any information required prior to attending will be provided closer to the workshop.