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Updated Practical 3 Processing 16S rRNA amplicon data (markdown) authored by Ben Francis's avatar Ben Francis
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## DADA2
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. Before we begin, there's one more thing we need to download, which is the formatted silva database used by DADA2 to assign taxonomy.
Before we begin, there's one thing we need to download, which is the formatted silva database used by DADA2 to assign taxonomy.
$ cd /bioinf/home/your_username/day_1/16S_amplicons/demultiplexed
$ wget https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1
### 3.1 Processing our data with DADA2
Now to get going with DADA2. First let's open up R again.
Now to get going with DADA2. DADA2 is a very large software with an entire integrated pipeline that takes raw reads (minus primers and barcodes) as input. It also needs lots of dependencies to do all of it's things. So in order to avoid wasting several hours installing it, I have a version of R with everything installed that you'll be using for this practical.
$ R
$ /home/tfrancis/R-3.6.2/bin/R
and if you're not already there, go to the data:
......