part 1 2019 - given on 02/27/2019

notes from 2018

part 2 03/07/2018

2018 dada2 exercise

2018 - More details on dada2 R Package

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
    2. Download RStudio
  2. Install these R packages ahead of time

    1. tidyverse from CRAN
    2. dada2 from Bioconductor
    3. phyloseq from Bioconductor
    4. ShortRead from Bioconductor
  3. See setup details at

  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 , you will need to download the Mothur MiSeq data from this link

  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 and put them into the “C:\dada2\MiSeq_SOP” directory

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

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