Annotation

Keywords

GFF3, Populus-tremula, RNA-Seq, Annotation

Authors

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

Type

• Lecture

Description

This introduces to the different sources of genomic and genic annotation and to their most commonly used format. It also introduces how to ensure that the used annotation are not a source of bias in downstream analyses.

Aims

Understand how to retrieve annotations; Learn about the different formats; Understand the effect of annotations on the results of downstream analyses

Prerequisites

• HTS-Introduction
• R-programming
• Unix

Target audience

From undergrade on, provided that the prerequisites above are fulfilled

Learning objectives

• Learn about the different annotation sources
• Learn how to retrieve an annotation set
• Learn how to curate an annotation set

Materials

• Lecture PDF and associated R examples in the corresponding folder

Data

• The data availability is described in the Dataset section
• and in the corresponding course

Timing

1h (lecture) + 2h (practical)

Content stability

Stable

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
• R (>=3.1), Bioconductor(>=3.0)

Literature references

• Robinson, Delhomme et al.
• Bioconductor