Nicolas Delhomme and Bastian Schiffthaler

Keywords

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

Authors

• @delhomme
• @bastian

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

Description

This merely lists the various courses at which we taught RNA-Seq data
pre-processing and analysis:

October 2014 EMBO course

Aims

Detailled in the corresponding courses:
1. October 2014 EMBO course

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

Prerequisites

Detailled in the corresponding courses:
1. October 2014 EMBO course

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

Detailled in the corresponding courses:
1. October 2014 EMBO course

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 |