I have three libraries with 100 barcodes each. Many barcodes are redundant between libraries. I need to create a combined OTU table for all three libraries.
I tried to merge the input at different steps of my QIIME 1 pipeline, but failed. What i am doing now is replacing redundant barcodes with unique ones, create a new mapping file and run all three libraries together in split_libraries. Is there a better way?