When Silva database was made compatible for MOTHUR, I found that to fish out 27f and 1492r primer region, screen.seqs command was used with start=1044 and end=43116. why these two start and end position was taken?
They are the positions right after the 27f primer and right before the 1492r primer. The “best practice” is to not include primer sequences in sequencing the 16S rRNA gene because you can get non-specific annealing if the primer has a mismatch at the 5’ end of the primer. If we required sequences to have the 27f/1492r primers, we would lose far more sequences.
Pat
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