Simon Morvan

Hello @benjjneb, Thank you for your quick reply and your help on the matter ! I will try it with cutadapt based on what you did with the ITS pipeline....

I've just tried using cutadapt to remove all the versions of the primers and their reverse complements. A higher proportion of the reads merge but I still lose a lot...

Here is the output: rbind(FWD.ForwardReads = sapply(FP1.orients, primerHits, fn = fnFs.filtN[[1]]), FWD.ReverseReads = sapply(FP1.orients, primerHits, fn = fnRs.filtN[[1]]), REV.ForwardReads = sapply(RP1.orients, primerHits, fn = fnFs.filtN[[1]]), REV.ReverseReads = sapply(RP1.orients, primerHits, fn...

Absolutly, Script 1 is the original script I used based on your recommandation. [Script1.docx](https://github.com/benjjneb/dada2/files/7462068/Script1.docx) I've also tested Script 2 after talking to a bio-informatician who advised me to only put...

Hi Ben, Have you had the time to check if something was off with the sequences or with how I was treating them ? Although I loose a lot of...

Hi @gcuster1991, in my case I continued on with my analyses as the rarefaction curves were looking okay. It's still a bit frustrating to keep such a small percentage of...

Hello Zachary, Thanks for your quick answer! I've tried to adapt the code to my parsed_phyloseq object but I still can't get it to work. When i run the calc_taxon_abund()...

Hi Zachary, sorry for the late answer. The piece of code you sent did not work. : ``` meta_obj$data$tax_ab