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Exome I: Intro
The purpose of this exercise for you to become familiar with the workflow used to analyze targeted sequencing data.
Your task is to identify possible disease causing mutation for a patient with Alpers syndrome.
Write a report where you shortly describe the different steps taken to identify the mutations, include details you may consider important. At the end of the report, list your candidate genes and outline how you ended up with such list.
Answers to marked questions with a 'Q', are for you to explore different output files, you do not need to include them in the report
Our data involves exome sequencing data from an affected individuala with Alpers syndrome (which is a progressive neurodegenerative disorder) and one control sample from a healthy individual.
You can find the article here.
| Sample | Description |
|---|---|
| AS_2 | Affected |
| AS_ctrl | Unaffected |
Connect to the server using MobaXterm (PC users) or your local Terminal (MACS users):
ssh -X your_account@rudy.biomedicine.gu.se
Set the environment:
cp /home/teacher3/.bashrc .
source .bashrc
Copy and untar exome.tar.gz from /home/teacher3/. Have a look at the different folders.