Duplicate barcodes on different sequencing runs

Hi all,

I have a project in which samples were sequenced on multiple runs (e.g.20 runs), which means some samples' barcode sequences are the same.

I am wondering whether I can generate one big mapfile with all samples included and then import all samples into qiime and continue the standard qiime2 pipeline without importing and DADA2 them 20 times based on their sequencing runs and combine them later. I heard that this method worked as all samples in that big mapfile have a unique sample ID in front of barcode sequence column.

My concern is if the barcodes are the same, they might get incorrectly assigned. But I also prefer to process these samples consistently (same cut-off to trim bad quality reads, same sampling depth) as they are from the same project.

Can I ask whether anyone has any opinions on this?

Thank you so much in advance!
Best Regards,
Godric Wang

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