Demultiplexing error for CASAVA, Paired End format

[Nicholas_Bokulich]

@Mehrdad

In my eyes, I do not think so I have dual index read. I have barcode in two side of amplicons (not each reads). Can I continue the rest protocol the QIIME2 tutorial? What do you think?

No. Barcodes on each side of the amplicon is the definition of dual-indexed reads. QIIME 2 does not have a method to demultiplex this. @thermokarst has already answered this and recommended a path forward:

@thermokarst

Unfortunately, QIIME 2 does not currently support demultiplexing dual-indexed reads. It sounds like from your post above that that is what you have — please correct me if I misunderstood. If you do have dual-indexed reads (barcodes in the forward and reverse reads) you will need to demultiplex these reads outside of QIIME 2 and then import them using a demultiplexed format (like the manifest format we discussed a few days ago).