Microbiome Analysis - dada2 Tutorial - part 1

part 1 2019 - given on 02/27/2019

• Github repo for dada2 tutorial https://github.com/vhertzb/dada2-lesson
• HTML lesson and presentation http://htmlpreview.github.io/?https://github.com/vhertzb/dada2-lesson/blob/master/dada2_workflow.html

---

notes from 2018

part 2 03/07/2018

• files for part 2 of the dada2 exercise at located in the Github repo at https://github.com/vhertzb/2018Week8

• See lecture in HTML at https://cdn.rawgit.com/vhertzb/2018Week8/master/2018Week8.html

2018 dada2 exercise

• see vhertzb Github repo at https://github.com/vhertzb/2018Week7

• HTML file with notes https://cdn.rawgit.com/vhertzb/2018Week7/05bff59a/2018Week7_dada2.html

2018 - More details on dada2 R Package

• dada2 homepage https://benjjneb.github.io/dada2/

Prep Work for dada2 Tutorial - Instructions from 2018

However, if you would like to come and work along with us through the exercises (hands-on), please come prepared with the following:

1. A laptop with R and RStudio installed:

   1. Download R https://cran.r-project.org/
   2. Download RStudio https://www.rstudio.com/products/rstudio/download/#download

2. Install these R packages ahead of time

   1. tidyverse from CRAN https://cran.r-project.org/web/packages/tidyverse/index.html
   2. dada2 from Bioconductor https://www.bioconductor.org/packages/release/bioc/html/dada2.html
   3. phyloseq from Bioconductor https://bioconductor.org/packages/release/bioc/html/phyloseq.html
   4. ShortRead from Bioconductor http://bioconductor.org/packages/release/bioc/html/ShortRead.html

3. See setup details at https://cdn.rawgit.com/vhertzb/2018week6/master/HW3_for_2018.html

4. Open RStudio – create a new project for this dada2 exercise – put it somewhere on your hard drive with a logical location, like "c:\dada2"

5. Then following along with the dada2 tutorial at https://benjjneb.github.io/dada2/tutorial.html , you will need to download the Mothur MiSeq data from this link http://www.mothur.org/w/images/d/d6/MiSeqSOPData.zip

6. One you download the ZIP file, extract all of the files. There will be a subfolder called “\MiSeq_SOP” – copy this folder and its contents into the project folder you created above (e.g. “c:\dada2”)

7. Next download, these 2 files “silva_nr_v132_train_set.fa.gz” and “silva_species_assignment_v132.fa.gz” from https://zenodo.org/record/1172783#.Wo2GM62ZMo8)https://zenodo.org/record/1172783#.Wo2GM62ZMo8https://zenodo.org/record/1172783#.Wo2GM62ZMo8) and put them into the “C:\dada2\MiSeq_SOP” directory

---

Copyright © Melinda Higgins, Ph.D.. All contents under (CC) BY-NC-SA license, unless otherwise noted.

Feedback, Comments (email me)?