2 materials found

Scientific topics: Data architecture, analysis... 


High-throughput sequencing training materials repository

This repository includes training materials on the analysis of high-throughput sequencing (HTS) data, on the following topics: Introduction to HTS, RNA-seq, ChIP-seq and variant calling analysis. Materials have been annotated following the standards and guidelines proposed at the “Best practices...

Scientific topics: Data architecture, analysis and design, Bioinformatics

Keywords: High throughput sequencing analysis, Rna seq chip seq anayses, Variant calling

High-throughput sequencing training materials repository https://tess.elixir-europe.org/materials/high-throughput-sequencing-training-materials-repository This repository includes training materials on the analysis of high-throughput sequencing (HTS) data, on the following topics: Introduction to HTS, RNA-seq, ChIP-seq and variant calling analysis. Materials have been annotated following the standards and guidelines proposed at the “Best practices in next-generation sequencing data analysis” workshop which took place at the University of Cambridge, UK, on 13-14 January 2015. Following this workshop, a Git repository has been set up for sharing annotated materials. This repository uses Git, hence it is decentralized and self-managed by the community and can be forked/built-upon by all users. Data architecture, analysis and design Bioinformatics High throughput sequencing analysis, Rna seq chip seq anayses, Variant calling Life Science Researchers PhD students Trainers beginner bioinformaticians post-docs 2015-12-17 2017-10-09
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