Oops! You mention above that you had already demultiplexed your data:
But from your screenshot, it looks like the data you imported is not demultiplexed.
If you are already running bcl2fastq
, it might be easiest for you to demultiplex your data with that tool, and then import the resulting demultiplexed files into QIIME 2 using a manifest format.
We are also working on implementing a q2-cutadapt
plugin, which will support demultiplexing paired end data that have barcodes still in the forward reads, so you could also wait for that to land (theoretically in the upcoming 2017.12 release).
Let me know if you have any questions! Thanks!