Demultiplexing multiple marker genes with overlapping barcodes

[jairideout (Jai Ram Rideout)]

Just noticed this is a duplicate topic. Locking this topic and moving further support here:

Multi-gene amplicon sequences with dada2

Hello, We amplified four gene markers (16S, 18S, 23S, rbcL) for each sample and combined all four markers before adding the barcode and sequencing. I now have demultiplexed sequences but each sample still contains sequences of all four amplicons. Do I need to create individual files for each sample and marker before processing with dada2? Each amplicon is a different size but I figure I can use the primer to parse them out. Is there anything in place to assist me with this? Thanks, Danny