cse185-spring19
Course website for CSE 185 Spring 2019
See the course syllabus for more details.
Resources
Lecture slides will be posted here 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 Gradesource Course CSE185-SP19
See Jupyter Assignment Instructions to get started with the labs.
See Final Project Guidelines for information about final projects. Also see Week 8 slides with additional tips and guidelines.
See Resources for more helpful resources each week.
Schedule
| 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 Week 1 resources |
| 2 | Genome assembly | Intro to assembly | More assembly - filling the gaps | So where do all those reference genomes come from, anyway? Quiz 1 Cheat sheet |
| 3 | Population genetics | Intro to pop gen | GWAS and p-values | GWAS-How tall should I be? Week 3 resources |
| 4 | RNA-seq | Intro to RNA-seq | Differential expression | You are what you eat Quiz 2 Cheat sheet |
| 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 Quiz 3 Topics list |
| 7 | Proteomics | Proteomics +mass spec intro | Mass spec database search | CSI: Proteomics |
| 8 | Projects | Project tips and guidelines | Special topic #1: Deep Learning | Independent projects |
| 9 | Projects | Memorial Day - no lecture | Special topic #2: Genome editing | Independent projects |
| 10 | Projects | Special topic #3: Complex variants | No lecture | Independent projects |