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Day5 - Read Mapping and Visualization

Welcome to Day 5 of the Short-Read Sequencing Analysis Workshop.The videos for day 5 will give you an introduction to read mapping. Video1 will go over how most short-read mapping programs work and show you how to index a reference sequence (genome) for both Bowtie and BWA. Videos2 and 3 will go over the mapping programs Bowtie and BWA, and Video4 will introduce you to the program IGV which can be used to visualize your alignment data.

Day 5 Videos

Video1: Introduction to Mapping This video gives some general background about how mapping is performed and will show you how to index your reference sequence with both Bowtie and BWA. Additionally, you will be introduced to the SAM and BAM file format that mapping programs output and how to do some basic manipulations/conversions of these files with Samtools. Slides for Video1

Video2: Using Bowtie and Bowtie2 Video2 goes over some of the differences between Bowtie and Bowtie2, when each is most appropriate, and some of the basic alignment and output/reporting options for both programs. Slides for Video2

Video3: Using BWA Video3 will introduce you to the different mapping algorithms contained within BWA. We will go through using the BWA aln algorithm and some of the options including working with single-end or paired-end read data. Slides for Video3

Video4: Using IGV for visualization The final video will show you how you can visualize your mapping data using IGV. This program can be used to view your mapping data alongside qualitative data such as annotations. You will also be introduced to BEDTools, which can be used to manipulate .bed files. Slides for Video4

Day 5 Files 

Day5 In-class slides (available by the start of class)

Day5 Homework (available by the start of class) 

Day5 Homework solutions (available the day after class)

Additional Resources 

Video on Burrows-Wheeler Transform

Video on short-read alignment (seed and extension)

Bowtie Paper

Bowtie Manual

Bowtie2 Manual

Samtools website

BEDTools website

IGV website

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