Welcome to CSE 185!

Note: for Spring 2021, this course will be held entirely remotely and materials will be available asynchronously. No in person attendance is required.

See the course syllabus for more details and the calendar for an overview of upcoming meetings and assignments.

Resources

All lectures will be held by Zoom. You should be able to join using this link. Links to lecture slides and recordings are below. You should also be able to find them saved on Google Drive.

All assignment Jupyter notebooks can be accessed via datahub.ucsd.edu.

We will use Piazza for discussions about assignments. Sign up here.

All grades will be posted to Canvas.

See also:

Jupyter assignment instructions to get started with the labs
Quiz policy
Final project guidelines [example papers used for projects from previous years]
Final project sign up document
UNIX commands cheatsheet
Lab session queue
Lab notes
Quiz 1 keys
Quiz 2 keys
Quiz 3 keys
Extra resources and reading material

Schedule

Week	Topic	Lecture 1	Lecture 2	Assignment
1	Intro/NGS	Course overview + NGS intro [Zoom]	NGS alignment and variant calling [Zoom]	Python lightning course (optional) Week 1 Survey (optional)
2	More NGS	Sources of error [Zoom]	Data visualization [Zoom]	Lab 1: NGS and mutation hunting (due 4/11)
3	Assembly	Intro to assembly and kmers [Zoom]	More assembly + long reads [Zoom]	Lab 2: Genome-size estimation and assembly (due 4/18) Quiz 1 [Review Info]
4	Population genetics	Intro pop gen [bonus slides] [Zoom]	GWAS [bonus slides] [Zoom]	Lab 3: Population genetics (due 4/25)
5	Transcriptomics	Intro to RNA-seq [Zoom]	Differential expression [Zoom]	Lab 4: Transcriptomics (due 5/2) Quiz 2 [Review Info]
6	Epigenomics	ChIP-seq and epigenomics [Zoom]	Motif analysis [Zoom]	Lab 5: Epigenomics (due 5/9)
7	Single cell	scRNA-seq overview [Zoom]	scRNA-seq analysis [Zoom]	Lab 6: Single-cell RNAseq (due 5/16) Quiz 3 [Review Info]
8	Comparative genomics	Bioinformatics and COVID-19 [Zoom]	Phylogenetics [Zoom]	Lab 7: Phylogenetics and COVID-19 (due 5/23) Project Proposal (due 5/21)
9	Final Projects	Project meetings	Project meetings	Work on final project
10	Final Projects	Project presentations	Project presentations	Work on final project
Finals week	Final Projects	No lecture	No lecture	Final Project due 6/11