Contact us
Lead Instructor Dr. Gene Yeo
Teaching Assistant Olga Botvinnik
Teaching Assistant Jamison McCorrison
All other lecturer contact info provided below.
Course Description
Quantitative Methods in Genetics and Genomics is designed to teach experimental and analytical approaches in modern genetics and genomics, from experimental design through data analysis in each of several topic areas. Lecturers this year include Gene Yeo, Scott Rifkin, Bruce Hamilton, Rob Knight, Olivier Harismendy, Nicholas Schork, Aaron Chang and Hannah Carter.
This course is a requirement for students in the UCSD Genetics Training Program. 4 units.
Syllabus
| Module Num. | Tues | Thurs | Lecturer | Topic | |||
|---|---|---|---|---|---|---|---|
| 1 | 1/5/16 | 1/7/16 | Olga Botvinnik, Gene Yeo (contact) | TSCC Setup, UNIX, Git/Github, and Python introduction | Lecture | Homework | Solution |
| 2 | 1/12/16 | 1/14/16 | Scott Rifkin (contact) | Statistic; logic of testing hypotheses; estimation | Lecture conda install R fix |
Homework | Solution |
| 3 | 1/19/16 | 1/21/16 | Bruce Hamilton (contact) | Low throughput methodology, qRT PCR | Lecture | Homework | Solution |
| 4 | 1/26/16 | 1/28/16 | Olga Botvinnik, Gene Yeo | NGS Technology, RNA-seq tools and analyses, IGV | Lecture Powerpoint Lecture | Homework | Solution |
| 5 | 2/2/16 | 2/4/16 | Rob Knight (contact) | Microbiome | Lecture evolution.py Additional Materials | Homework | Solution |
| 6 | 2/9/16 | 2/11/16 | Olivier Harismendy (contact) | NGS sequencing. Analysis file standards. SNPs and SNVs in cancer. Querying public databases. Variant annotation, filtering and statistical associations. | Lectures: NGS Tools, Practice - Day 1 Practice - Day 2 | Homework | Solution |
| 7 | 2/16/16 | 2/18/16 | Gene Yeo, Olga Botvinnik, Jamison McCorrison | Review of class materials. | Lecture | Homework | Solution |
| 8 | 2/23/16 | 2/25/16 | Nicholas Schork (contact) | Modern Applied Population Genetics. Applied Population Genetic. Admixture Mapping. | Lecture 1 Exercise 1 : Python/PLINK Exercise 1 : R/Plots | Homework | Solution |
| 9 | 3/1/16 | 3/3/16 | Hannah Carter (contact) | Genome-wide associations studies. | Lectures: Exercise 1, Exercise 2, Exercise 3, Exercise 4, Powerpoint 1, Powerpoint 2, Data | Homework | Solution |
| 10 | 3/8/16 | 3/10/16 | Hannah Carter | Prioritizing genetic variation. Inherited variation. Somatic variation. | Lectures: Exercise 1, Week 2 Lecture, pptx | Homework | Solution |
Tips and tricks
- FAQ from homework 1 (ssh, logging in to TSCC< starting up a notebook, file navigation)
- Git essentials
- Fixing unreadable notebook error
- Nano keyboard shortcuts
Class Location
All lectures throughout the quarter will be held in the Sanford Consortium for Regenerative Medicine (SCRM) building.
- For the first week of the quarter (1/5 and 1/7), the class will be held in the second floor auditorium. This is the large auditorium besides the Bella Vista Cafe on the second floor.
- For the remainder of the quarter, all lectures will be held in the first floor conference room (#1013).
- All rooms have been reserved from 8:45 am to 12:15 pm.
- Class will start promptly at 9:00 am.
Final
Take home exam due Monday March 14, 2016