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 |