---
tags: ggg, ggg2021, ggg201b
---

# Syllabus for GGG 201(b) lab section: Genomics (Winter 2020/2021)

UC Davis

## URL: http://bit.ly/2021-ggg-201b-syllabus

### GitHub archive: [github.com/ngs-docs/2021-GGG201b-lab](https://github.com/ngs-docs/2021-GGG201b-lab)

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## Code of Conduct

Please abide by [my lab's Code of Conduct](http://ivory.idyll.org/lab/coc.html) in this course.

In particular, this is not an intellectual contest, and please realize that we all have plenty of things to learn.

## Lab sessions

What: hands-on computational work
When: Friday 9-10:50am
Where: Zoom via Canvas.

## Attendance and recordings

Lab sessions (on Friday) will be recorded and saved for a month, in Canvas. Please ask if you can't find one!

Attendance is expected. Please let Dr. Brown know if you can't attend; note there's no need to say anything more than "I can't attend on this Friday."

## Homework

There will be three homeworks, submitted via GitHub Classroom (I will explain what this is at the time). Details to be announced.

Homeworks can be done collaboratively, but you need to hand it in individually.

The goal of the homework is for you to complete it. 100% of people who asked for help on the homework in 2020 got full credit. Please reach out.

## Grading and collaborative work

I grade each homework S/U. The division of grading between labs and the rest of the course is in the whole course syllabus.

You are welcome to work with others on any aspect of the lab, but you must hand in your assignments on your own.

## In-class chat via Slack

We'll use Slack for sharing links and commands in lab. Please visit ucdavis.slack.com to create an account, and then join the slack channel `#2021-ggg201b-lab`.

## Office hours

Office hours for Titus are 2-4pm on Tu and Thu. Please schedule via this link:
https://calendly.com/ctitusbrown/office-hours.

My office hours will take place in my zoom room, zoom.us/my/titusbrown/.

## Instructors

C. Titus Brown (IOR) (<[e-mail]>)

## Lab description

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:

1. familiarize you with the basic operational concepts involved in variant calling, genome assembly, and RNAseq differential expression.
2. introduce the use of workflow management tools as a core aspect of biological data analysis.
3. 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](https://hackmd.io/3zFfz02TTGm4117qwy1xNg?view).

## Schedule of lab topics

Weeks 1-4 - snakemake workflows for variant calling.
* [lab 1 - intro, workflows, snakemake, and variant calling](https://github.com/ngs-docs/2021-GGG201b-lab/blob/latest/lab-1.md)
* [lab 2 - more snakemake, more variant calling](https://github.com/ngs-docs/2021-GGG201b-lab/blob/latest/lab-2.md)
* [lab 3 draft - variat calling](https://hackmd.io/phFaKouETICSS3ms6I-1CA?view)

Weeks 5-7 - Assembly.

Weeks 8-10 - RNAseq differential expression.

Lab walkthroughs and homeworks will be made available [on github](https://github.com/ngs-docs/2021-GGG201b-lab).