All documentation for the class is best viewed from the github.io pages
Overview
Genomic analyses require Bioinformatics skills. Therefore, the first part of the course is a tour through 3 critical technologies every genome analyst needs: Unix/Linux, R, and Python. In the second part of the course, you will use your newfound skills to perform experiments in RNA-Seq, variant detection, metagenomics, etc.
Instructors
BIS180L is normally taught by Dr. Julin Maloof, but Dr. Maloof is on sabbatical so the instructors and course content are different this quarter.
- Ian Korf - Professor in MCB and Genome Center
- Nikhil Joshi - Analyst at the UCD Bioinformatics Core
- Lilith Marinho-Davis - TA from IGG program (and Ian’s lab)
Discord
The class has a Discord Channel. The instructors monitor the Discord channel, so if you have a question outside of classroom hours, this is a good place to ask. Please join the Discord server here: https://discord.gg/QTsBfMNp75
Office Hours
You can schedule a 30 min session with the professor via Calendly. https://calendly.com/iankorf/zoom
Grading
Each unit ends with a graded written assignment. The grade depends on several factors.
- Completeness - the degree to which all the questions were answered
- Correctness - the degree to which the answers are correct
- Neatness - the overall organization of the text, figures, and documents
- Togetherness - citizenship within the class (you are expected to come to class, interact with people, and collaborate with your lab partner)
There is no final exam for the course because you are graded on assignments on a regular basis.
Content
- Introduction to the command line
- Introduction to R
- Introduction to Python
- RNA-Seq
- Pairwise Alignment
- Variant Detection
- Metagenomics