Genetics 760: Genomic Methods for Genetic Analysis

Course Organizer: Jim Noonan: james.noonan@yale.edu

TAs:Tim Johnstone: timothy.johnstone@yale.eduCarina Gerveshi: carina.gerveshi@yale.edu

Course Wiki: we will email this to you

Genetics 760:Objectives

• Intro to genome analysis and interpretation• How to address biological questions from a genomic perspective

• Analyze data from high throughput sequencing applications- ChIP-seq- RNA-seq- Whole exome sequencing- Metagenomics- Big functional genomics datasets

Genetics 760:Objectives

• You will learn how to:

- Work with massive datasets in a Linux HPC environment

- Write your own scripts in Python and R to parse files, run pipelines, do basic statistical analyses

- Understand, design and interpret genomic analyses

- Use genomics data to gain biological insights

Genetics 760: Components

• Lectures on topics in genomics- Introduction to computational methods- Accessing genomes- High throughput sequencing technologies- Gene expression, regulation and epigenetics- Genetic variation in genes and regulatory elements- Metagenomics and proteomics- Large genome survey projects (ENCODE)- Genomics of human disease

Genetics 760: Components

• Problem sets and Friday Discussion sessions

- PS#0 and PS#1: Intensive introduction to the Linux environment and scripting, and working with

genomic data

- We will primarily use Python in this course. Your firstassignment is to take the ~13-hour intro to Python

course at Codecademy: www.codecademy.com. We expect you to have done this by the time PS#1 is due.

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Genetics 760: Components

• Problem sets and Friday Discussion sessions

- PS#2-4: Applications of genomics datasets

• Analyzing regulomics data (ChIP-seq, epigenetics)• Analyzing transcriptome data• Discovery and interpretation of whole-exome

variation

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Genetics 760: Components

• Final Project:

- Team-based, collaborative analysis of an original genomic question

- This will occupy the last month of the course (April – early May)

- You will have access to the TAs, but will be workinglargely independently

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Genetics 760: Advice

• If you have no experience, the learning curve in the first month or so will be very steep: do not get discouraged

• This course will take more time than you are used to

• Communicate effectively with your TAs- Ask specific questions- Explain exactly what you are trying to do and what is

not working- Keep careful track of your workflow- Take the initiative and exclude obvious problems before

you ask the TAs to debug your code

Information we need from you

• Your name• Your netID• A non-Yale email account• Your Grad School year• Are you taking the course for Credit or are you an Auditor?

• Your level of experience with:- Working in a UNIX/Linux environment- High performance computing- Scripting in Perl or Python- R- Any other programming language- High-throughput sequencing apps or data

In a single email to james.noonan@yale.edu: