Demultiplexing Reads
Overview
Teaching: 0 min
Exercises: 0 minQuestions
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 minQuestions
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 minQuestions
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 minQuestions
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 minQuestions
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: minQuestions
Objectives
Key Points
Beta diversity
Overview
Teaching: 0 min
Exercises: 0 minQuestions
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 minQuestions
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