As you have correctly identified, your barcodes are in your files, so MultiplexedPairedEndBarcodeInSequence
makes sense to use.
But!
The I1 and I2 are Index 1 and Index2 for your forward and reverse reads. I would expect the barcodes to be inside these files, so these are necessary and need to be included!
Dear Colin,
thank you for the fast reply. Actually, the barcodes are not part of the read sequences.
I have two separate barcodes files I1 and I2. And R1 and R2 for the reads.