Hi, I’ve tried to trim Silva db v.132 ( which size ~10 Gb) by primers pair:
I made the reverse compliment of the reverse primer and generated file oligos.txt which looks like:
forward GAGTTTGATCMTGGCTCAG reverse CCAGCAGCCGCGGTAAW
And run mothur with the following commands:
pcr.seqs(fasta=silva.nr_v132.align, oligos=oligos.txt, pdiffs=2, rdiffs=2)
In both case
pcr.seqs() returned an empty file “silva.nr_v132.pcr.align” and file “silva.nr_v132.scrap.pcr.align” with the same size like the original silva.nr_v132.align file.
After that I’ve tried to repeat this manipulations with Silva SEED db, but result was the same.
And one more, I also tried to reproduce the example from the topic and got the same result which I’ve described - empty *pcr.align file.
mothur version is 1.41.1 (linux)
What I’m doing wrong?