I´m new to the sequencing world but am planning a 16s amplicon sequencing with two variable regions.
Therefore I´m trying to set up a pipeline and bioinformatic workflow, before I start my experiment to be on the safe side.
I think sidle/the SMUFR algorithm will fit my approach and went through the tutorial.
The primers I would like to use and that are suggested in literature by for example Parada et al 2016 contain Ys,Ms,Ws,Rs,Hs etc..
Now I am wondering if I can prepare a "regional database for each primer set" and extract the regions from the database with these non biological primer sequences or will that be a problem.
If so, do you have any advice how to deal with that?
Thank you very much!