Course website for CSE 185 Spring 2020
Under construction!!* This page is no longer being maintained. All material will be updated on Canvas this quarter. Note: for Spring 2020, due to the COVID-19 situation, this entire course will be held remotely. No in-person attendance is required.
See the course syllabus for more details.
Lecture slides and zoom recordings will be posted here and on Canvas throughout the quarter.
Assignments will be posted each week on our course JupyterHub at datahub.ucsd.edu.
We will use Piazza for discussions about assignments.
Grades will be posted on Canvas.
- Jupyter Assignment Instructions to get started with the labs.
- Quiz policy for more info about quizzes.
- Final Project Guidelines for information about final projects.
- Resources for more helpful resources each week.
|Week||Topic||Lecture 1||Lecture 2||Lab Assignments|
|1||Intro to NGS||Course overview + NGS intro||NGS alignment and variant calling||Mutation hunting - find the needle in a haystack due 04/05/20 (no penalty up to 04/12/20)|
|2||Genome assembly||Intro to assembly||More assembly + long reads||So where do all those reference genomes come from, anyway?
|3||Population genetics||Intro to pop gen||GWAS||Predicting height from your genome|
|4||RNA-seq||Intro to RNA-seq||Differential expression||You are what you eat
|5||ChIP-seq||ChIP-sequencing and epigenomics||Motif analysis||The dark matter of the genome|
|6||Single cell||scRNA-seq overview||scRNA-seq analysis||Don’t get lost in the crowd
|7||Comparative Genomics||Comparative Genomics Intro||Phylogenetics||Tracking COVID-19|
|8||Projects||Project tips and guidelines||Proteomics+mass spec||Independent projects|
|9||Projects||Memorial Day - no lecture||Special topic #1: Deep Learning||Independent projects|
|10||Projects||Special topic #3: Diversity in human genomics||No lecture||Independent projects|