How to check which 16S variant region the reads targets? by saying that I could not obtain the sequencing information from anyone. This forum is the last place I could find help. Another question, could qiime2 combine and process two sets of data targeting different variant regions? Thank you!
I’m not sure I understand the question. Are you trying to figure out what primers were used to amplify data? Or trying to figure out which part of a database primers amplify?
I am trying to figure out which part of the 16S sequence were amplified? V3, V4…?
I have a couple of ideas, but none of them are particularly easy. Obviously, getting the information from the primary source would be easiest. If you know the primer pair or positions, you can look it up. Again, if you can get the primer pair fom the person who did the sequencing, this is best. Anything else you do it a guess.
So, that said, if you have reads where the primer is not trimmed, you could try aligning them to get the primer sequence, and then searching that for positions and region. If you don’t have that in your files and you don’t have any other primer/label information, I think you are out of luck. Even if your data is trimmed, you should be able to combine multiple regions in the same sample using the workflow the community developed for ion torrent:
If you’re working in meta analysis (1 region/sample but combining multiple regions), but best recommendation would be closed reference OTU clustering although others prefer fragment insertion and taxonomic analysis on features collapsed to genus level.