Recently, I used trim.seqs using the following oligos file, which contains the degenerate forward prime, the 3 variations of forward primer, and the reverse:
I used the following command:
trim.seqs(fasta=sortedseq.pick.fa, oligos=/Volumes/GriffenLeysLab/Daniel/database/noreversemiseq.oligos, pdiffs=2, processors=6)
The problem I am having is that the trim.seqs recognizes the forward and reverse primers and still scraps the primers not meeting my parameters. However, some of the obtained sequences still have the forward primer in them.
Is this a bug or do you have any suggestions?
P.S. I reran the trim.seqs on output file from produced trim.seqs file using an oligos file only containing the 3 variations of the primer and it looks like it trims the primer sequences off while still retaining the sequence: