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Before we begin, there's one thing we need to download, which is the formatted silva database used by DADA2 to assign taxonomy.
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$ cd /bioinf/home/your_username/day_1/16S_amplicons/demultiplexed
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$ wget https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1
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$ wget https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz
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### 3.1 Processing our data with DADA2
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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.
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