I didn’t dumtiplex in qiime1 actually. Once you have the forward, reverse, and barcodes files it is easier to just import them into Qiime2 and do the rest of the analysis, including demultiplexing, there.
Have a look through the Atacama-soils tutorial which shows the whole process of starting with the multiplexed F, R, and barcode reads. The example sample-metadata file they are using has a column named “BarcodeSequence” which is being referred to in the
--m-barcodes-column option. So you’ll need to make your own metadata file (see here for more detail info on that) and include a column where you list your Forward and Reverse indexes as they appear in your barcodes.fastq.
Depending on your data and how your facility hands you the data you might have to play around with the orientation of these to make sure they are in the same order. see qiime
demux emp-paired --help for some extra options in the event your sequences are not in the expected order.
Also, see this little explanation to make sure your reads match the expected criteria.
FYI, the importing can be one of the most confusing part of qiime2 because there are hundreds if not thousands of different ways you can have your data and that that is facility/user-specific. But once you’re in Qiime2 everything becomes much much easier. So, don’t give up and good luck!