Hello! I've sequenced samples with the IDT xGen 16S Amplicon Panel v2 and was trying to analyze our results with the ampliseq multiregion option, but I keep getting empty files after dada2 (too few reads after trimming), so SIDLE starts running with no input. As input I used the primers as provided by the manufacturer one for each region, although some of these have degenerate primers (in which case I only used the pair that has the most matches in SILVA) It seems this (or similar) questions have been posted before, but no conclusion was reached, any idea on how we could proceed? or is this pipeline incompatible with this kind of samples?

It seems this (or similar) questions have been posted before, but no conclusion was reached, any idea on how we could proceed?

I am unsure what you are referring to.

or is this pipeline incompatible with this kind of samples?

from the description you posted here the data should be fine to the pipeline (I didnt check the links).

although some of these have degenerate primers (in which case I only used the pair that has the most matches in SILVA)

That might be a problem, primers should be given to the pipline as they were used for the PCR.

too few reads after trimming

If after primer removal (cutadapt) too less reads, the primers were not appropriate or the data is lacking. If after DADA2's filterntrim are too less reads, and its a read quality issue consider increasing https://nf-co.re/ampliseq/2.17.0/parameters/#max_ee or such, or maybe the region_length is too small.

Thank you so much, sorry for the unclear details, this kit uses a mix of primers to amplify all 16S variable regions, some of the primer pairs are degenarate which would either force the reference primers tsv to have duplicate sequences per primer pair or to include some primers with 8+ degenerate bases. After looking into your DADA2 parameters, I suspect the lengths in the reference tsv table might be too short, meanwhile I'll try changing the max_ee parameter