I’m having trouble in getting Mothur to locate my primer(s) and barcodes when using trim.seqs. Thus only 8 of my >20000 sequences went into trim.fasta and the rest went into scrap. The reason for scrapping most sequences seems to be unlocated primer and barcode.
I was using command: trim.seqs(fasta=H88XYFD01.fasta, oligos=arch.oligos, qfile=H88XYFD01.qual, maxambig=0, maxhomop=10, minlength=50)
My .oligos file looks like this:
barcode AGCGCGCGC Tit-B-Arch349F_101_SB4
barcode AGCTCTATC Tit-B-Arch349F_102_CC2
barcode ATAGACATC Tit-B-Arch349F_103_MM3
And here is an example of a sequence that went into the .trim.fasta file:
And here are 2 examples of sequences that went into the scrap file because barcode and primer were not located (although I was able to locate them manually).
How should I modify my command so that the primer and bar code can be located. Allow mismatches?