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 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,CC-BY-NC-SA unless otherwise noted.

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