analyzing plates with the same barcode combination

[dcopetti]

Hello, I am planning to run PacBio 16S Kinnex on a set of six 96-well plates and I wonder how to set up the analysis when there will be files obtained from the same barcode combination.

The 16S Kinnex setup has up to 384 different primer combinations (4 plates), so e.g. plates 5 and 6 will have the same barcode combination/name as plates 1 and 2. There will be two libraries (with different barcoded adapters), made with two sets (1-3 and 4-6) of plates, so I will do two demultiplexing jobs separately (first adapter, then the barcode in the primers), resulting in 576 fastq files.

Do you think there will be any issues with barcode combination when setting up the configuration files for this pipeline? It would be great if you have any tip on how to analyze 6 plates in a single job. Thanks, Dario