Partial sequence of reverse primer

Commands in mothur
1

I am working with pyrosequencing data. We have sequences a fragment of 16S that is approximately 400bp in length. Originally we assumed that we would not reach the reverse primer, however one of my collaborators thinks that its possible there might be portions of the reverse primer left in some of the sequences.

I was wondering if it’s possible to search for partial sequence of the reverse primer - for example variable lengths of the reverse primer, and trim them from the sequence?

from the trim-seqs command, it sounds like I would need to have the an exact match to the primer sequence, so I’m not sure if it’s possible.

Thank for your help.

2

The easiest way to deal with this is likely in the filter.seqs command with trump=. If many of your sequences do not make it to the reverse primer, then when you use filter.seqs with trump=., the reverse primer sequence will go away.

Does that help?
Pat