Materials from Intro to Bioinformatics lab, Winter offering at UC Davis (Jan-Mar 2022)
To the extent possible under law,
Titus Brown
has waived all copyright and related or neighboring rights to
GGG 201(b), Winter 2021 at UC Davis.
This work is published from:
United States.
Please abide by my lab's Code of Conduct in this course.
In particular, this is not an intellectual contest, and please realize that we all have plenty of things to learn.
What: hands-on computational work
When: Friday 9-10:50am
Where: Zooooooom!
There will be three homeworks, submitted via GitHub Classroom.
Homeworks can be done collaboratively, but you need to hand it in individually.
I grade each homework S/U. The division of grading between labs and the rest of the course is in the whole course syllabus.
C. Titus Brown (IOR) (ctbrown@ucdavis.edu)
You can sign up for office hours using this calendly link, or e-mail Titus at ctbrown@ucdavis.edu.
In this lab, we will build and examine three different automated workflows, for three common bioinformatics tasks: variant calling, genome assembly, and RNAseq differential expression. (These will not be cutting edge workflows and should not be directly used for your own work, but they will be complete and functional.)
The overall learning goals for the lab are to:
- familiarize you with the basic operational concepts involved in variant calling, genome assembly, and RNAseq differential expression.
- introduce the use of workflow management tools as a core aspect of biological data analysis.
- describe scientific issues surrounding data analysis techniques and processes, including statistical issues, reproducibility, provenance, and publication.
In terms of technology, we'll be using the snakemake workflow system, running on the farm cluster. We'll touch briefly on git/GitHub and conda, but those topics will be gone into in much more detail in GGG 298.
- 1/7 - Intro; variant calling 1