This is a very simple question. I have received some reads which I am not sure if they still contain primers, adapters or any type of non-biological sequences. I want to first check if these non-biological sequences exist, and secondly remove them before downstream analysis. Is there a straightforward way to perform the mentioned tasks in Qiime?
I knew the region so I just took commonly used primers and searched in the opened in browser .qzv file for partial sequences of those primers. In my case I confirmed that primers are deleted and proceeded with the analysis.
The easiest one-step procedure may just be to run q2-cutadapt without looking. If primers or adapters are present, you will see a reduction in read length. If not, then there should be no effect!
You would need to export the sequences and look at them directly.
tabulate-seqs can’t help you here, since it requires a FeatureData[Sequence] artifact as input. You can only examine the fastq sequences by exporting them from QIIME 2. Nothing wrong with that… just export and then search for your primer sequences. One reason to just use q2-cutadapt for this is that it will perform a search for degenerate primers so that you don’t need to.