Importing and Demultiplexing: Multiplexed Paired-End Fastq with Forward and Reverse Barcodes

Hi there,

I have R1, R2, I1, I2 (fastq.gz folders) for a total of 671 samples. Below is a image with an example for 4 samples:

I'd like to import and demultiplex them but I'm not sure of the best approach. From previous discussions, I'm thinking of combining the forward and reverse barcodes with, so I could use the EMP Paired-End Protocol with a single barcode.

However, the above would only do the job for 1 out of the 671 samples. I was thinking of constructing a massive 'PairedEndFastqManifestPhred33' file for all samples. But then again, the manifest format doesn't seem to take barcodes into account.

Given my situation, what is the most appropriate and efficient way to import and demultiplex them? Thank you for this amazing platform and all the kind responses.

Hello YinXun,

I think this is a great idea!

I think that’s OK. The barcodes let you seperate your reads by sample, but your reads are already separated by file name, so the barcodes are not needed anymore.


EDIT: It’s PairedEndFastqManifestPhred33V2 now. Take a look the examples.


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