This folder contains the necessary files and data to run the DADA2 pipeline in R. For this course we will mainly use Rstudio when running , which you already should have installed R. Also make sure that you have installed the necessary packages.
- Make a working directory for the DADA2 pipeline on your computer
- Optional: Make an R-project in your working directory
- Download the R script either from Rstudio (type in the console):
download.file("https://raw.githubusercontent.com/krabberod/BIO9905MERG1_V21/main/Dada2_Pipeline/DADA2_pipeline.R", "DADA2_pipeline.R") - Or the boring way DADA2_pipeline.R
- Open the script in Rstudio
- Make as subdirectory called fastq in the working directroy
- Download the fastq files to the subdirectory (link is in the script)
The fastq files have already been processed:
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The samples have been demultiplexed, i.e. split into individual per-sample fastq files.
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Primers and adapters and have been removed.
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Paired-end data has been matched in the same order (i.e. sequences in the R1 and R2 fastq files arein the same order)
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A link can be found in the DAD2 script
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If you didn't manage to finish the pipeline during hands-on an RData image of the full pipeline has been added to the repository containing all the necessary results from the pipeline: dada2.RData
This can be downloaded and the opened i Rstudio:
load("dada2.RData")
The script is based on the DADA2 tutorial https://benjjneb.github.io/dada2/tutorial.html