I wish to use Cutadapt in Qiime2 to trim primers from demultiplexed, paired-end data that has reads for two different amplicons (a mix of 16S and 12S amplicons from vertebrate DNA in each sample).
Is it possible to trim F and R primers from both amplicons using Cutadapt in Qiime 2?
I have done it in the past with the standalone Cutadapt by first running a command with the primers from the first amplicon, and having all reads that were not trimmed (did not possess these primers) output to a separate directory. Then I would run a command with the primers from the second amplicon on the untrimmed directory. This would allow me to trim primers for both amplicons, and separate reads from each amplicon for each sample.
Is it possible to do something similar to this in Qiime2? If so how?
On a more general note, when I have amplicons from different regions I process them separately. You could do this too by using the deblur plugin to filter out just the 16S reads and just the 12S reads.
In the cutadapt plugin setting, there is an output for the trimmed sequences:
But I don’t see how to also output the untrimmed sequences?
How would I output the untrimmed reads to a separate directory so that I can process them a second time in cutadapt to remove the primers from my second amplicon?
Hey there @Trodgers! As @colinbrislawn mentioned, you might make the quickest progress by using cutadapt directly (fortunately it is already installed in your QIIME 2 env!). We have an open issue regarding this missing output: