Hi @VerheulJulia,
I am a little confused. This could be my lack of expertise in Trimmomatic but I am not sure how Trimmomatic provided a file containing sequences that had successfully paired? I looked through the docs and I couldn't find any mention of the merging sequences in the documentation. I looked at the demux file and those sequences are not merged so I am just a little confused.
If you are looking to trim out adapters, I would recommend cutadapt because it stays in the qiime2 system and your commands would be tracked through provenance. :qiime2:
I asked for your primers so that I could calculate the rough sequence length of your sequences. Most of the time sequences do not merge because they are not long enough to have overlap.
I am alittle confused about your primers and this might be effecting trimming:
This is a 806R primer. This is typically the end of the of v4 region.
This is the reverse complement of the above adapter. So It doesn't look like you have the beginning adapter.
I hope that helps!
