Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

adding amplicon skeleton outline #41

Closed
wants to merge 1 commit into from
Closed

adding amplicon skeleton outline #41

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
41 changes: 40 additions & 1 deletion 13-microbiome.Rmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
ottrpal::set_knitr_image_path()
```

# Microbiome Sequencing
# Amplicon Microbiome Sequencing

<div class = "warning">
This chapter is incomplete! If you wish to contribute, please [go to this form](https://forms.gle/dqYgmKH8XXE2ohwD9) or our [GitHub page](https://github.com/fhdsl/Choosing_Genomics_Tools).
Expand All @@ -14,6 +14,45 @@ 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






Expand Down