Finding Causative Mutations With A Candidate SNP Approach.

In this lesson we will look at the powerful technique of Mutational Genomics. This is possibly the coolest thing ever as it involves mutating a living organism so that it is different from other things and then sequencing the genome to pinpoint the exact changes that cause the difference.

Prerequisites

For this course you are going to need to know some basic genetics (an Intro or 101- style course will do) and you’ll need to know some of the basic outputs from High-throughput sequencing (HTS) machines. Try these links for information.

1. EBI Train online - NGS (HTS)
2. Wikipedia - Molecular basis of inheritance

In this lesson we don’t have the scope or chemicals to do the mutation bit, so we’ll pick up with the genomics and use Galaxy and Galaxy tools to carry out the analysis that takes us from sequence data to actual candidate mutations in the genome sequence.

This lesson will use a virtual machine (a small computer-within-a-computer) system to get you a working install of Galaxy and all the data that we need for the lesson.

Getting ready

It is absolutely imperative that you have downloaded and installed these two items:

1. Virtual Box software from https://www.virtualbox.org/
2. The lesson specific virtual machine GCC2015-CandiSNP.ova from Google Drive
3. You can also download these course materials for offline viewing from this GitHub link

Topics

1. Why Do We Need Mutational Genomics?
2. Mutagenesis and Genetic Screens
3. Pre-Processing Sequence Data
4. Aligning Reads To A Reference
5. Finding SNPs With An Alignment
6. Visualising SNPs To Find Candidates

Other Resources

• Reference