Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material

Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material

Keywords

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

Authors

  • Nicolas Delhomme (@delhomme)
  • Bastian Schiffthaler (@bastian)

| Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references |

Description

Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these guidelines and reproduces the Differential Expression analysis conducted in Robinson, Delhomme et al., 2014.

Aims

Understand the principles of an RNA-Seq analysis. Learn about data pre-processing and Quality Assessment. Learn about RNA-Seq limitations and analysis caveats.

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Prerequisites

  • HTS-Introduction
  • R-programming
  • Statistics
  • Unix

Target audience

From undergrade on, provided that the prerequisites above are fulfilled

Learning objectives

  1. Introduction
  2. Quality Control
  3. Alignment
  4. Annotation
  5. Expression-estimation
  6. Differential-expression
    • What is a differential expression analysis
    • How to assess the quality (the biological meaningfulness) of the count data
    • What is a confounding factor
    • How to identify a confounding factor
    • How to block a confounding factor

| Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references |

Materials

  • EMBO October 2014 - Tutorial
  • EMBO October 2014 - Introduction
  • EMBO October 2014 - QC
  • EMBO October 2014 - Alignment
  • EMBO October 2014 - Annotation
  • EMBO October 2014 - Expression-estimate
  • EMBO October 2014 - Differential-expression

Data

### Description
Uses the dataset Robinson, Delhomme et al., 2014

Availability

Detailed in the dataset Robinson, Delhomme et al., 2014

Top | Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references

Technical requirements

  • Best is to use our Docker (a self contained environment) based on the Bioconductor NGS Docker that can be used to setup the course machines (physical or in the cloud)
  • Otherwise:
  • a UNIX OS
  • FastQC
  • SortMeRna (>= 1.9)
  • Trimmomatic (>=0.32)
  • STAR (>=2.4.0)
  • R (>=3.1), Bioconductor(>=3.0)

Literature references

  • Robinson, Delhomme et al.
  • SortMeRna
  • Trimmomatic
  • STAR
  • Bioconductor

| Keywords | Authors | Description | Aims | Prerequisites | Target audience | Learning objectives | Materials | Data | Technical requirements | Literature references |

Scientific topics: RNA-Seq

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

Authors: Nicolas Delhomme @delhomme, Bastian Schiffthaler @bastian

Nicolas Delhomme - Bastian Schiffthaler - October 2014 EMBO course material https://tess.elixir-europe.org/materials/nicolas-delhomme-bastian-schiffthaler-october-2014-embo-course-material Material for the course held on EBI Campus, Welcome Trust Center, Hinxton, UK on 20-26th, October 2014. The material cover general RNA-Seq data pre-processing as described in these [guidelines](http://www.epigenesys.eu/en/protocols/bio-informatics/1283-guidelines-for-rna-seq-data-analysis) and reproduces the Differential Expression analysis conducted in Robinson, Delhomme et al., 2014. RNA-Seq FASTQ, GFF3, BAM, Populus-tremula, RNA-Seq, Pre-processing, QC, Alignment, Annotation, Expression-estimation, Differential-expression, R-programming