preparing sequence files for mothur

I am trying to analyze my miseq illumina run on mothur, but I am not sure where to start. Our pcr libraries were formed using combinations of a forward primer with a barcode and a reverse primer with an index, we had 8 unique barcodes and 16 unique reverse primers. Our sequencing company demultiplexed our sequences based on the reverse index, therefore I have 16 different fastq files, which each contain the sequences for 8 different samples that have unique barcodes. Do you have any suggestions on how I should proceed? From the tutorials it appears that I need to have 1 fastq file per sample, but I am not sure how to separate my files to do that. Any help would be appreciated.

Alma - you should be able to proceed with the MiSeq SOP. You’ll have to create a files file that tells make.contigs which files go together for each sample.