Difference of the types for importing data

[Nicholas_Bokulich]

@Marine_Microbiology

1, If the data has its own forward/reverse sequences files, but with the barcode in, do I still consider them as demultiplexed data?

No, those are not demultiplexed. See this tutorial to see how to demultiplex sequences that are barcodes inside the sequences.

@Marine_Microbiology

3, I guess the ‘MultiplexedPairedEndBarcodeInSequence’ type is also for demultiplexed data, what are the differences between ‘MultiplexedPairedEndBarcodeInSequence’ and ‘EMPPairedEndSequences’?

The difference is essentially just that whether the barcode is part of the sequences or in its own separate sequence file.