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Course website for CSE 185 Spring 2020
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README.md

cse185-spring20

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.

Resources

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.

See

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 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?
Quiz 1
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
Quiz 2
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
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
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