Alignment of RNA-Seq data

Keywords

Alignment

Authors

Bert Overduin (@bert)

Type

• Lecture
• Practical

Description

Focus on BAM format

Aims

Provide a worked example of aligning your reads to a reference genome

Prerequisites

• Introduction to NGS
• Linux
• Quality control
• general knowledge of molecular biology

Target audience

beginner, biologist

Learning objectives

• Producing alignment of reads to a reference genome
• Recognizing the challenges and pitfalls
• Interpreting the aligners output

Materials

Part of the Edinburgh genomics introduction to RNA-seq data analysis

Data

• SRP019027
• Forward reads
• Reverse reads

Timing

Lecture + tutorial: 1.5h

Content stability

Stable. Date of last major update of the materials: 2014-11-24.

Technical requirements

• TopHat
• Bowtie

Literature references

• None