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UCSD CSE 185

Advanced Bioinformatics Laboratory

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 an external site.. Links to lecture slides and recordings are below. You should also be able to find them saved on Google Drive Links to an external site..

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

We will use Piazza for discussions about assignments. Sign up here. Links to an external site.

All grades will be posted to Canvas.

Schedule

Week	Topic	Lecture 1	Lecture 2	Assignment
1	Intro/NGS	Course overview + NGS intro Download Course overview + NGS intro [Zoom Links to an external site.]	NGS alignment and variant calling Download NGS alignment and variant calling [Zoom Links to an external site.]	Python lightning course (optional) Week 1 Survey (optional)
2	More NGS	Sources of error Download Sources of error [Zoom Links to an external site.]	Data visualization Download Data visualization [Zoom Links to an external site.]	Lab 1: NGS and mutation hunting (due 4/11)
3	Assembly	Intro to assembly and kmers Download Intro to assembly and kmers [Zoom Links to an external site.]	More assembly + long reads Download More assembly + long reads [Zoom Links to an external site.]	Lab 2: Genome-size estimation and assembly (due 4/18) Quiz 1 [Review Info]
4	Population genetics	Intro pop gen Download Intro pop gen [bonus slides Download bonus slides] [Zoom Links to an external site.]	GWAS Download GWAS [bonus slides Download bonus slides] [Zoom Links to an external site.]	Lab 3: Population genetics (due 4/25)
5	Transcriptomics	Intro to RNA-seq Download Intro to RNA-seq [Zoom Links to an external site.]	Differential expression Download Differential expression [Zoom Links to an external site.]	Lab 4: Transcriptomics (due 5/2) Quiz 2 [Review Info]
6	Epigenomics	ChIP-seq and epigenomics Download ChIP-seq and epigenomics [Zoom Links to an external site.]	Motif analysis Download Motif analysis [Zoom Links to an external site.]	Lab 5: Epigenomics (due 5/9)
7	Single cell	scRNA-seq overview Download scRNA-seq overview [Zoom Links to an external site.]	scRNA-seq analysis Download scRNA-seq analysis [Zoom Links to an external site.]	Lab 6: Single-cell RNAseq (due 5/16) Quiz 3 [Review Info]
8	Comparative genomics	Bioinformatics and COVID-19 Download Bioinformatics and COVID-19 [Zoom Links to an external site.]	Phylogenetics Download Phylogenetics [Zoom Links to an external site.]	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

This course content is offered under a CC Attribution Non-Commercial Share Alike Links to an external site. license. Content in this course can be considered under this license unless otherwise noted.