2 min read

Module 7: Read mapping

2024-01-27

Overview

Module 7 focuses on the critical process of read mapping in genomics, where sequencing reads are aligned to a reference genome. This step is fundamental for various downstream analyses, including variant calling, expression quantification, and structural variant detection. The module will cover the principles of read mapping, the use of different alignment tools, and the visualization techniques to interpret the results. Practical labs will reinforce the concepts and provide hands-on experience with read mapping workflows.

Introduction

  • Definition and purpose of read mapping in genomics
  • Overview of alignment algorithms and their applications
  • Challenges in read mapping, such as repetitive regions and sequencing errors

Topics

Principles of Read Mapping

  • Understanding the alignment problem in bioinformatics
  • Sequence alignment algorithms: global, local, and semi-global
  • The role of scoring matrices and gap penalties

Mapping to Reference Genome

  • Preparing a reference genome for alignment
  • Overview of popular read mapping tools (BWA, Bowtie2, STAR)
  • Detailed walkthrough of the read mapping process
  • Optimization of mapping parameters for different sequencing data types
  • Handling paired-end and single-end reads

Post-Mapping Processing

  • Sorting and indexing mapped reads
  • Marking duplicates and removing artifacts
  • Understanding SAM/BAM file format and CIGAR strings

Visualization of Mapped Reads

  • Introduction to genome browsers and visualization tools (IGV, UCSC Genome Browser)
  • Visual interpretation of alignment results
  • Identifying common patterns and anomalies in mapped reads

Labs

  • Lab 1: Preparing the Reference Genome and Read Mapping with BWA
  • Lab 2: Post-Mapping Processing and SAM/BAM Manipulation
  • Lab 3: Visualization and Analysis of Mapped Reads using IGV

Learning Outcomes

By the end of this module, students will be able to:

  • Explain the significance of read mapping in genomic analyses.
  • Describe the principles behind alignment algorithms and their use in read mapping.
  • Perform read mapping to a reference genome using state-of-the-art alignment tools.
  • Conduct post-mapping processing to prepare data for downstream analyses.
  • Navigate and interpret SAM/BAM file formats and understand the information they convey.
  • Utilize genome browsers and visualization tools to analyze and present mapped reads.
  • Recognize and troubleshoot common issues in read mapping.