I have Illumina Miseq amplicon sequences that I need to demultiplex for use in qiime2. My library prep used a dual indexed method that allowed me to multiplex 4 separate gene markers (ie. 16S, 18S...) per sample. Each individual sample number has a tag that I can easily demultiplex, but I am having trouble demultiplexing the separate genes out of each sample. I figure I can use the primer pairs that were used in the original amplification step to parse out the 4 genes within each sample. Unfortunately, Qiime does not offer this in their demultiplexing tools. Can anyone point me in the right direction or have any tips on the best way to demultiplex my samples by both sample name and then by gene.