Well… This might sound stupid.
I have 2x300 MiSeq reads on 18S region, but the problem is, now, I have learnt that amplicon size is 634. Even without truncation, paired reads only reach 600 length so, I’m short of about 34 bp.
Maybe I understood the context completely wrong, so please help me understand it better.
Is there anything I can do to analyse the data or is it all trash? Can someone point me to a direction?
I’m completely lost on this subject…