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Content provider: GOBLET 

and

Authors: Jared Simpson  or Eija Korpelainen  or Maria Victoria .  or Julie Sullivan  or Friederike Ehrhart  or nekrut  or Boris Steipe  or Marie-Claude Blatter 


RNA-seq data analysis: from raw reads to differentially expressed genes

This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of...

Scientific topics: Sequencing, RNA, Data architecture, analysis and design, Bioinformatics

Keywords: Bioinformatics, Differential expression, Ngs, Rna seq

RNA-seq data analysis: from raw reads to differentially expressed genes https://tess.elixir-europe.org/materials/rna-seq-data-analysis-from-raw-reads-to-differentially-expressed-genes This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of 10-30 minute lectures intertwined with hands-on exercises, and it can be accomplished in a day. As the user-friendly Chipster software is used in the exercises, no prior knowledge of R/Bioconductor or Unix ir required, and the course is thus suitable for everybody. Our book RNA-seq data analysis: A practical approach (CRC Press) can be used as background reading. The following topics and analysis tools are covered: 1. Introduction to the Chipster analysis platform 2. Quality control of raw reads (FastQC, PRINSEQ) 3. Preprocessing (Trimmomatic, PRINSEQ) 4. Alignment to reference genome (TopHat2) 5. Alignment level quality control (RseQC) 6. Quantitation (HTSeq) 7. Experiment level quality control with PCA and MDS plots 8. Differential expression analysis (DESeq2, edgeR) -normalization -dispersion estimation -statistical testing -controlling for batch effects, multifactor designs -filtering -multiple testing correction 9. Visualization of reads and results -genome browser -Venn diagram -volcano plot -plotting normalized counts for a gene -expression profiles 10. Experimental design Sequencing RNA Data architecture, analysis and design Bioinformatics Bioinformatics, Differential expression, Ngs, Rna seq Bench biologists Life Science Researchers 2015-12-04 2017-10-09
STAO 2014 Understanding a genetic disease thanks to Bioinformatics

This workshop allows to discover several bioinformatics tools and databases (genome browser, alignment tool, BLAST, dbSNP, UniProtKB, PDB) in the context of the discovery of a rare variant leading to the production of a non functional insulin in a Norwegian family. Additional documents are ...

Keywords: Blast, Genome browsing, Introduction bioinformatics, Protein structure visualisation, Variant detection

STAO 2014 Understanding a genetic disease thanks to Bioinformatics https://tess.elixir-europe.org/materials/stao-2014-understanding-a-genetic-disease-thanks-to-bioinformatics This workshop allows to discover several bioinformatics tools and databases (genome browser, alignment tool, BLAST, dbSNP, UniProtKB, PDB) in the context of the discovery of a rare variant leading to the production of a non functional insulin in a Norwegian family. Additional documents are available: http://education.expasy.org/cours/Toronto Blast, Genome browsing, Introduction bioinformatics, Protein structure visualisation, Variant detection high school 2014-11-10 2017-10-09