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Day 5: Introduction to Read Mapping and Visualization

Day 5: Introduction to 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.

Videos for Day 5

** Please note these videos are from 2015. The software versions may have changed but the concepts and basic pipelines remain the same.

Video1: Introduction to Mapping (14:46)  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.

Video2: Using Bowtie and Bowtie2 (13:18)  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.

Video3: Using BWA (8:03)  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. 

Video4: Using IGV for visualization (12:25)  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. 


Day 5 Files 

Day 5 In-class Slides

Homework for Day 5 

Day 5 Homework Answers


Additional Resources 

Video on Burrows-Wheeler Transform

Video on short-read alignment (seed and extension)

Bowtie Manual  Links to the manual for Bowtie

Bowtie2 Manual  Links to the complete manual for Bowtie2

Samtools website  This website has the downloads, as well as links to documentation including the manual

BEDTools website  The website for BEDtools has the downloads as well as documentation

IGV website  The IGV website has all of the documentation for the program as well as downloads for installation

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