Pcr.seqs nomatch=keep not giving expected output

Commands in mothur
1

Hi,
I’m running pcr.seqs in mothur v. 1.48 on a custom database using the following command

pcr.seqs(fasta=custom_db.align, processors=8, keepdots=F, keepprimer=T, seed=8947961, start=1044, end=13862)

which leads to roughly 1/6 of my sequences to end up in the bad.accnos file. I assume this is because their start > requested start and/or end < requested end?

I was under the impression setting nomatch=keep would keep these sequences in the pcr.align file, but what it actually does is print the full 50.000bp sequence (instead of position 1044-13.862) to the scrap.pcr.align. Is this the intended behaviour? Is there a way to allow sequences with leading/trailing dots to not be rejected?

2

The nomatch parameter is only used by mothur when you are using an oligos file. You can use the chops.seqs command to trim while allowing for leading/trailing gaps.

First trim from 13862:
chop.seqs(fasta=current, keep=front, countgaps=true, numbases=13862)

To trim to position 1044 (13862-1043):
chop.seqs(fasta=current, keep=back, countgaps=true, numbases=12819)