Register training material
1327 materials found

Lecture slides for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Lecture slides for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/lecture-slides-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Introduction to HTS

No description available

Keywords: HTS-introduction

Introduction to HTS https://tess.elixir-europe.org/materials/introduction-to-ngs No description available HTS-introduction
EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014

No description available

Scientific topics: RNA-Seq

Keywords: FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming

EMBO High Throughput Sequencing Data Analysis, Cambridge, UK, 2014 https://tess.elixir-europe.org/materials/embo-high-throughput-sequencing-data-analysis-cambridge-uk-2014 No description available RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming
NGS introduction to file formats

This sub-module gives an overview of the most used file formats in Next Generation Sequencing analysis

Keywords: HTS-introduction, FASTQ, BAM, VCF, WIG, CRAM, GFF3

NGS introduction to file formats https://tess.elixir-europe.org/materials/ngs-introduction-to-file-formats This sub-module gives an overview of the most used file formats in Next Generation Sequencing analysis HTS-introduction, FASTQ, BAM, VCF, WIG, CRAM, GFF3
Exploratory analysis and downstream analysis

This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods...

Keywords: Statistical-model, Exploratory-analysis

Exploratory analysis and downstream analysis https://tess.elixir-europe.org/materials/exploratory-analysis-and-downstream-analysis This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods developed (e.g.) for microarray data. Statistical-model, Exploratory-analysis
Quality Control

This is an introduction to the tools available for performing the technical QA of RNA-Seq data and to their results, singling out possible common caveats.

Scientific topics: RNA-Seq

Keywords: FASTQ, RNA-Seq, Pre-processing, QC

Quality Control https://tess.elixir-europe.org/materials/quality-control This is an introduction to the tools available for performing the technical QA of RNA-Seq data and to their results, singling out possible common caveats. RNA-Seq FASTQ, RNA-Seq, Pre-processing, QC
NGS introduction to sequencing platforms

This sub-module gives an overview of the most used sequencing platforms and their applications.

Keywords: HTS-introduction

NGS introduction to sequencing platforms https://tess.elixir-europe.org/materials/ngs-introduction-to-sequencing-platforms This sub-module gives an overview of the most used sequencing platforms and their applications. HTS-introduction