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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

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Course website for CSE 185 Spring 2019

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