1. Genetics 760: Genomic Methods for Genetic Analysis Course Organizer: Jim Noonan:james.noonan@yale.edujames.noonan@yale.edu TAs: Tim Johnstone:timothy.johnstone@yale.edutimothy.johnstone@yale.edu Carina Gerveshi:carina.gerveshi@yale.educarina.gerveshi@yale.edu Course Wiki:we will email this to you

2. 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

3. 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

4. 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

5. 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 first assignment 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.www.codecademy.com 5

6. 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 5

7. 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 working largely independently 5

8. 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

9. 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: