This lesson is still being designed and assembled (Pre-Alpha version)

Microbial Amplicon Analysis

Demultiplexing Reads

Overview

Teaching: 0 min
Exercises: 0 min
Questions
  • How do I demultiplex reads from different samples?

Objectives
  • Understand how read barcodes function

  • Demultiplex reads from several samples into separate files

Exercise: Demultiplex a small set of reads by hand Exercise: Use a computational tool (FIXME: Which?) to demultiplex a small dataset. (Does not have to be the same one as later lesson steps.)

Key Points

  • Barcodes let us sequence many samples at the same time and separate them computationally

  • Most pipelines require demultiplexing reads as a first step


Sequnece quality control

Overview

Teaching: 0 min
Exercises: 0 min
Questions
  • How do I get my sequences ready to count?

Objectives
  • FIXME: ADD OBJECTIVE

  • FIXME: ADD OBJECTIVE

FIXME

Key Points

  • FIXME: ADD KEY POINT

  • FIXME: ADD KEY POINT


Counting microbes with QIIME2-Deblur

Overview

Teaching: 0 min
Exercises: 0 min
Questions
  • How do I tally microbes with QIIME2 and Deblur?

Objectives
  • FIXME: ADD OBJECTIVE

  • FIXME: ADD OBJECTIVE

FIXME

Key Points

  • FIXME: ADD KEY POINT

  • FIXME: ADD KEY POINT


Counting microbes with DADA2

Overview

Teaching: 0 min
Exercises: 0 min
Questions
  • How do I tally microbes with DADA2?

Objectives
  • FIXME: ADD OBJECTIVE

  • FIXME: ADD OBJECTIVE

FIXME

Key Points

  • FIXME: ADD KEY POINT

  • FIXME: ADD KEY POINT


Counting microbes with mothur

Overview

Teaching: 0 min
Exercises: 0 min
Questions
  • How do I tally microbes with mothur?

Objectives
  • FIXME: ADD OBJECTIVE

  • FIXME: ADD OBJECTIVE

FIXME

Key Points

  • FIXME: ADD KEY POINT

  • FIXME: ADD KEY POINT


Overview

Teaching: min
Exercises: min
Questions
Objectives

Key Points


Beta diversity

Overview

Teaching: 0 min
Exercises: 0 min
Questions
  • What is beta diversity and how do I calculate it?

  • How can I plot beta diversity and interpret the results?

Objectives
  • Understand what beta diversity means from an ecology standpoint

  • Understand the most common methods of beta diversity calculations, including their relative strengths and weaknesses

  • Be able to plot beta diversity and interpret the results

  • Be able to perform cluster analysis on beta diversity and interpret the results

Exercise: Describe what Beta Diversity means from an ecology standpoint. (In an Etherpad?) Exercise: Calculate beta diversity using Bray-Curtis ordination and plot Exercise: Calculate beta diversity with Weighted/Unweighted Unifrac and NMDS and plot. Explain the differences amongn them Exercise: Perform cluster analysis on the above beta diversities to identify clusters in the data

Key Points

  • Beta diversity measures the diversity between samples in a dataset

  • The most common beta diversity measures are Bray-Curtis, Weighted/Unweighted Unifrac, and NMDS

  • Beta diversity is usually displayed as a principal coordinates plot

  • Cluster analysis can identify groups of samples, but care must be taken to be sure the groups are meaningful


Finding Differentially Abundant Microbes

Overview

Teaching: 0 min
Exercises: 0 min
Questions
  • How do I find whicih microbes are different in different samples?

Objectives
  • FIXME: ADD OBJECTIVE

  • FIXME: ADD OBJECTIVE

FIXME

Key Points

  • FIXME: ADD KEY POINT

  • FIXME: ADD KEY POINT