I have been used mothur 454 SOP several times withou any problem. Now I have one 454 Junior run, which is not of excellent quality (lot of short reads,but there are also some which are ok) and I have some problems with trim.seqs command. After trimming all my sequences felt to scrap files, with the indication |bf in my fasta file, indicating that there was not possible to find primer and barcodes in shhh.fasta file. But when I checked this, I found them in all sequences… I tried to use trim.seqs with or without option flip=T, minlength=200 or even =100, but the results are same (I sequenced from reverse primer, but as I said, I can recognize it in my shhh.fasta reads, but not in shhh.trim.fasta).
Do you have any idea what can be wrong? Can you help me somehow?