I have 454 data (16S V1-V3 regions) in which there seems to be a non-100% match between the forward and reverse sequences. In general, I can say that we retrieve more reverse sequences, and that the reverse sequences show some species we do not obtain with the forward sequences (and vice versa, but relatively more with the reverse ones).
Now my questions to you, guys ('n' gals):
How do you process forward and reverse sequences? Take the average? Add them up and work with relative frequencies, ... ? How would you handle this aberration?
What are your experiences with pyrosequencing both forward and reverse? Do you think you get enough information using only 1 primer but perhaps get some more sequences from a sample? Or do you feel using both primers is really necessary?