Hi there!
I was going through the SOP for “MOTHUR”. I found an option “trump” for the command “filter.seqs”. When I searched for the command (http://mothur.org/wiki/filter.seqs/#trump), I become confused with the “NOTE” here in the link.
It will be of great help if anyone please make me clear about the command and the specific option?
If you follow the sequence of using screen.seqs and then filter.seqs as described in the MiSeq SOP, you’ll be in good shape. The note is telling you that you need to make sure that your sequences overlap a common region before using trump=. in filter.seqs
Pat
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