Mapping Quality Control

Keywords

Alignment, BAM, QC

Authors

Bert Overduin (@bert)

Type

• Lecture
• Practical

Description

Perform QC on aligned data

Aims

Understand the importance of quality control aspects of alignment and perform the QC.

Prerequisites

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

Target audience

beginner, biologist

Learning objectives

• Applying QC software and interpreting the output
• Deciding/performing necessary filtering steps

Materials

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

Data

• Original 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

• samtools

Literature references

• None