Course Structure, NCSU

Module 5

By Carlos C. Goller

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.

We want you to be successful in using the HPC and submitting a QIIME2/DADA2 job. Please watch the series of videos we have included on the course website. These videos describe the difference between the use of OTUs and ASVs for amplicon-based metagenomics, introduce you to the HPC, and provide a tutorial on how to use QIIME. We will also be available to help you! Post questions to the Student Help forum and come to virtual hours. Together we will use the HPC to analyze large datasets.

Do not forget to read and annotate the third paper. The analyses discussed in this study tie directly to the tools we will use in this module. Read, annotate, and respond to the module Top Hat questions.

We are close to the end of the course, pay attention to the deadlines, and continue working on your data analysis projects, BIT 577 tutorial, and creative podcast. We appreciate your hard work and know you will create valuable resources for others and learn how to analyze microbial communities in the process! 

BIT 477/577 Metagenomics F20 Mixtape 5
BIT 477/577 Metagenomics F20 fifth mixtape recording.

Meta Mix 5 mp3

 

Things To Come by Broke For Free is licensed under an Attribution-NonCommercial-NoDerivatives (aka Music Sharing)