Import multiplexed paired-end - 3 files per sample

I am trying to import illumina data where I have 3 files per sample - forward, reverse and barcodes. Do I import each sample separately (using EMP protocol) and later merge them? Or merge first and then demultiplex?

Hi @jem1101,

It sounds like your sequences are already demultiplexed so you don’t need to worry about that. As so, you won’t need the barcode files either.
Simply follow the importing tutorial here for importing demultiplexed files using a manifest. Good luck!


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