On 2/28 we are going to use dada2 to process demultiplexed, trimmed fastq files into something that can be use in phyloseq as an OTU table and analyzed to examine the microbiome. In order to follow along with this in class we ask that you prepare for it. Your homework is to show, in an rmd file on your repo that you subsequently output to pdf to turn into the Canvas site, that you have done this advance work. This takes some time, most of it just to have the machine process, hence the need to get it done before class.
Please document that you have installed the necessary packages and downloaded the appropriate files.
dada2 and phyloseq, as well as shortread and ggplot2. Use the installation guide at the dada2 site: (http://benjjneb.github.io/dada2/index.html)[http://benjjneb.github.io/dada2/index.html].library(package_name); packageVersion(“package_name”);
ggplot2, these packages are not available through CRAN; rather you will have to go through bioconductor. See the dada2 installation instructions for guidance. Note: you should already have ggplot2, but please document it as well.dada2 walkthrough page, the link marked “example data used in the Mother MiSeq SOP”. Unzip this dataset and store it on your computer.the RDP species assignmet set from the same site as the RDP training set. Again, do not unzip it but DO store it in the same directory as the miseq files.
You can provide evidence that you have downloaded these files with the following commands (in an R chunk):
path <- “~/MiSeq_SOP” # CHANGE THIS to the directory containing the fastq files after unzipping
fns <- list.files(path)
fns
Due on 2/28 at 5 pm.