From 03ed2decd50267967da044365e7557b834b5ef4d Mon Sep 17 00:00:00 2001
From: Chloe Herman <60228108+cherman2@users.noreply.github.com>
Date: Fri, 17 Nov 2023 15:31:38 -0700
Subject: [PATCH] add amplicon skeleton outline

---
 13-microbiome.Rmd | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/13-microbiome.Rmd b/13-microbiome.Rmd
index 4790f208..9f0cbd36 100644
--- a/13-microbiome.Rmd
+++ b/13-microbiome.Rmd
@@ -14,6 +14,43 @@ This chapter is incomplete! If you wish to contribute, please [go to this form](
 ```{r, fig.alt = "FIGURE CAPTION GO HERE", out.width = "100%", echo = FALSE}
 ottrpal::include_slide("GOOGLESLIDE GOES HERE")
 ```
+## Goals of Amplicon analysis
+
+## Data Collection and Processing of Amplicon Analysis
+- QIIME 2 is a bioinformatics microbiome analysis platform. QIIME 2 has all the 
+tools discussed in the course in one ENV. 
+    - There are currently 3 different interfaces: Python, CLI and Galaxy! 
+    - add cool features of QIIME 2 
+
+## Upstream Analysis
+
+### Demultiplexing
+
+### Quality Filtering
+- Dada2 
+- Deblur 
+- Cutadapt 
+
+
+## Downstream Analysis 
+
+### Phylogenetic Tree Construction
+
+### Rarefaction
+- Even sampling 
+- Relative frequency (?)
+
+### Alpha Diversity
+
+### Beta Diversity
+
+### Taxonomic Annotation
+### Differential Abundance  
+### Speciality Tools
+#### Longitudinal Data 
+#### Fecal Microbiota Transplant 
+#### Predictive Models
+