Trim.seqs with reverse MiSeq PE reads

using Mothur v.1.32.1
I am trying to use trim.seqs to pull out barcoded samples within a larger dataset and ultimately I would like to use make.contigs on those samples. I used the following trim.seqs command and example oligos file on the forward fasta and qual files and it worked beautifully, but I am having difficulties getting it to work with the reverse files.

trim.seqs(fasta=Forward.fasta, qfile=Forward.qual, oligos=barcode.txt, allfiles=t)


In my reverse files, the barcode is at the end of the sequence. If I open the fasta file and reverse complement it (barcode now at beginning of seq), the command works but then my qual file does not match (not reverse complemented). I have tried the command with a single barcode written either regularly or reverse complemented (similar to the one above) as well as with paired barcodes (barcode; seq1; seq2; sample1) but none works without reverse complementing the fasta. It seems as though I am not telling mothur to look in the right place for the barcode.

Why not use make.contigs on the whole dataset? Make.contigs will create a group file if you provide an oligos file. Then you could use get.groups to select the samples you want.

Mothur can give you the reverse of the quality file as well as a fasta file. reverse.seqs(fasta=yourFasta, qfile=yourQualityFile).