Course Structure

TopHat and Module 5

By Carlos C. Goller

Hello!

We hope you enjoyed the weekend and are ready for a new module in the course.

Podcast Script Review

Podcast scripts are due tomorrow night. Then, you will be able to access the scripts for peer review and feedback.

Please enter the names of those involved in the podcast for us to assign reviewers. Thank you and have a great weekend!

TopHat Issues

I made a mistake and set TopHat questions due tonight instead of tomorrow night. Do not worry. I am working to extend the deadline. If you can’t submit Module 4 questions, let me know.

Module 5 will address: What are OTUs and ASVs?

We will learn about 16S/ITS metagenomic analyses using QIIME2 and DADA2.

Checklist icon
Checklist icon in a gray box. Purchased from The Noun Project.

Our checklist for this week can be accessed here. (opens in new window)

Read article 3 this week and annotate with at least ten meaningful annotations.

This week we will open up the lab tomorrow for you to join if you want and complete the HPC activity posted on Moodle. You are not required to come to Jordan Hall, though it will be a place for you to work. You can work on the QIIME2/DADA2 assignment on your own in another place or come in and talk to peers.

Podcast scripts are due for scholar peer review this week. This is your chance to learn from others and proofread!

CG

Overview

What are OTUs and ASVs? In this module, we will learn about 16S/ITS metagenomic analyses using QIIME2 and DADA2.

Upon successful completion of this module, you will be able to:

  • MO 5.1. Compare and contrast OTUs and ASVs.
  • MO 5.2. Discuss and critically evaluate each step of a 16S QIIME standard operating procedure (SOP).
  • MO 5.3. Perform basic data analyses using QIIME and a downloaded dataset.
  • MO 5.4. Apply tools from QIIME tutorial to analyses of other data sets:
    • Create OTU tables to use for analyses in QIIME and elsewhere (e.g., R for plotting).
    • Use alpha and beta diversity tools to assess richness and diversity within and between samples.
    • Plot several different types of graphs using QIIME’s interface.
  • MO. 5.5. Define and explain the concepts of metadata, OTU, rarefaction curve.

To complete this module, you will need to:

  • Watch Module 5 video and complete Top Hat questions
  • Complete HPC training. Complete Top Hat questions on HPC/QIIME.
  • Annotate third article using Hypothes.is
  • Reading questions/ reflection in Top Hat.
  • Contribute to Class Notes.
  • Draft approach for the data analysis project.
  • Meet with Digital Media Librarian for podcast recording.