PacBio primer trimming

I am analyzing PacBio reads of insert (with barcodes/adaptors removed), but I have noticed some sequences have leading/trailing bases before the primers, which means trim.seqs won’t work. Additionally, some of the primers are truncated.

I didn’t see any mention of this here, so I am wondering if there is a mothur solution.



Unfortunately, there isn’t anything special we do. Usually if you set bdiffs or pdiffs sufficiently high, trim.seqs will get these edge cases.