How to deal with redundancy among master barcodes?

[VicenteFR]

Hi!

I closed the issue I'd opened recently since I realized it was a problem upstream in the process, up to the demultiplexing process (Checkout). As part of my barcodes.txt file, I have two samples with a redundant master barcode, as shown below.

Sample ID Master barcode sequence Slave barcode sequence S001 TAAGGCGAcagtggtatcaacgcagagtNNNNtNNNNtNNNNtct TCGACTAGacacsttkttcaggtcctc S005 TAAGGCGAcagtggtatcaacgcagagtNNNNtNNNNtNNNNtct TTCTAGCTacacsttkttcaggtcctc

Therefore, I wasn't capturing any reads for S005 when applying Checkout. However, I read your answer to this issue related to my problem and, as suggested, I did run Checkout again using the next format for my barcodes.txt file:

S001 TAAGGCGAcagtggtatcaacgcagagtNNNNtNNNNtNNNNtct TCGACTAGacacsttkttcaggtcctc S005 ttCTAGCTacacsttkttcaggtcctc TAAGGCGAcagtggtatcaacgcagagtNNNNtNNNNtNNNNtct

Nevertheless, again, I didn't capture any reads for S005, and end up having the double amount of reads expected for S001. So, did I misunderstand your answer in the referenced issue? Is there any possible format for Checkout to overcome the redundancy between my samples' master barcodes?

I would really appreciate your help @mikessh Thanks so much!