Updated Practical 3 Processing 16S rRNA amplicon data (markdown) authored by Ben Francis's avatar Ben Francis
## DADA2
DADA2 is an R package, and it's proved very difficult to install! So instead of using our normal R, we're going to use a version where we have DADA2 preinstalled. You'll find it in the course folder you downloaded earlier:
$ /bioinf/home/your_username/marmic_NGS2020/software/R/bin/R
Hopefully everyone managed to successfully install DADA2. It has a lot of functions and an entire integrated pathway that takes demultiplexed raw reads (minus primers and barcodes) as input. You should already be in R, but if not, just start it up again.
### 3.1 Processing our data with DADA2
First let's go back to our data directory
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