![]() The data for these samples can be found on the CME website. NOTE: If you are not working from microbe server, you will need to change the file paths for idemp and cutadapt to where they are stored on your computer/server.įor this tutorial we will be working with some samples that we obtained 16S amplicon data for, from a Illumina Miseq run. Software is working and set up some of the variables that you will need Once the packages are installed, you can check to make sure the auxillary Library( plotly) packageVersion( "plotly ") # enables creation of interactive graphs, especially helpful for quality plots # '4.8.0' Library( ggplot2) packageVersion( "ggplot2 ") # for creating the final graph at the end of the pipeline # '3.1.0' Library( Hmisc) packageVersion( "Hmisc ") # for creating the final graph at the end of the pipeline # '4.2.0' Library( tidyr) packageVersion( "tidyr ") # for creating the final graph at the end of the pipeline # '0.8.2' Library( dplyr) packageVersion( "dplyr ") # for manipulating data # '0.8.0.1' Library( ShortRead) packageVersion( "ShortRead ") # dada2 depends on this # '1.38.0' Library( dada2) packageVersion( "dada2 ") # the dada2 pipeline # '1.10.1' WARNING: This installation may take a long time, so only run this code if these packages are not already installed! Answer 'yes' twice in the console to continue. If this is your first time on Rstudio server, when you install a package you might get a prompt asking if you want to create your own library. Now, install DADA2 & other necessary packages. Then click dada2_fiererlab and dada2_tutorial_16S.R to open the R script. You can navigate to the proper folder in Rstudio by clicking on the files tab and navigating to the location where you downloaded the github folder. The R script is located in the tutorial folder you downloaded in the first step. Set up (part 2) - You are logged in to Rstudio on server (or have it open on your computer)įirst open the R script in Rstudio.
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