Hi,so I am working with 30 samples of 16s and they have this primers 341f/785r.I have demultiplexed them and I tried to use “cutadapt trim-paired” to remove the primers,another guy had worked with this before but he is not in the lab anymore,so I saw he wrote this Reads were trimmed the foward and reverse primer minimum length: 402 pb; maximun length: 429; minimum quality score: 25; degree of mismatching allowed: 0; homopolymers no longer than 10. Reads with ambiguous bases and singletons were removed. Chimera were checked and removed from the dataset with the consensus method. 1
I tried setting this parameters in galaxy but den I use demux summarize and i have 0 of everything,also how do I use qiime dada2 denoise-paired if I put the minimum lenth in the cutdap?thank you
Hi @camin,
I think that it would be helpful to back up a bit.
Can you please post the visualization for demux summarize after you had demultiplexed them?
I would also suggest searching the forum for the answers to questions similar to yours, its a great way to learn and get answers.
Also, this tutorial specifically for galaxy interface users might be worth a look!
--Hannah