trim.seqs to remove reverse primer

Commands in mothur
1

Hi,
My 454 data recovers reverse primers at 3’ end. I would like to trim both forward and reverse primers out in trim.seqs command. Do I just don’t add # in front of reverse primer line in oligos file? The reverse primer seq should be written in oligos in 5’-3’ direction?

Thank you,
arifch

2

I tried doing above but it didn’t work. Can mothur trim reverse primer seqs in 454 data?

3

The sequence has to end with the reverse primer for trim.seqs to find it and it needs to be in the 5’ to 3’ direction. One option for you would be to create a specialized version of silva.bacteria.fasta using pcr.seqs that does not include your primer sites. When you align the sequences, the primer regions will be trimmed.