I was using MiSeq 2 x 300 bp to sequence 16S rRNA v3-v4 region. However, I get some low qulity bases in the MIDDLE of the forward sequence.
And I could not merge the forward and reverse reads without lossing a lot of counts. So I have 2 ways to deal with that.
One, only use around 120 bp forward sequence. The other way is two use the joined forward and reverse sequence around 400bp, but with 15 ambiguous base paire. Both way, I saved more than 80% of my reads. But I do not know which one give the better result(e.g. diversity, taxa…). I assume the longer sequence with ambiguous base pair give the better result than shorter sequence.
Looking forward to your opinions!