sorry, i am new to mothur.can you show me how exactly how to " find your primer in the alignment and then see where your primers are mapping to" according to your previous answer. Using what kind of commands? i am right now using mothur in windows.
These are the positions within the silva.bacteria.fasta alignment. You would need to find your primer in the alignment and then see where your primers are mapping to. Alternatively, you could run pcr.seqs on an E. coli sequence with your primers, align the product to silva.bacteria.fasta and then run summary.seqs on the algined sequence. The start and stop would be the coordinates of what you want.
Look at what Juan is trying to do here…
I’m not sure which region of the silva reference database my primers cover, they are 27F forward and 519R, I saw a previous entry in the forum which said to run pcr.seqs on silva.bacteria.fasta using an oligos file including both the forward and revers primers and setting keepdots=T, then running summary.seqs on the output file.
I followed this procedure but my output silva.bacteria.pcr.fasta file is empty, what can I be doing wrong?
I entered this command:
mothur > pcr.seqs(fasta=silva.…