Hi, I have two fastq.gz files that are a forward "raw read" and a reverse "raw read." I also have the barcode tsv. How do I import the fastq files and demultiplex everything? I can manifest them in but that doesn't demultiplex it since I can't include the metadata in that way, right? Any help woul…

Hi @msport469 , Multiplexed reads with a separate barcodes fastq file can be imported and demultiplexed using the appropriate EMP format and qiime demux emp-paired — see the importing tutorial at qiime2.org for more details. Good luck!

thanks, but i have the barcode tsv not the barcode fastq. Is there a way around this?

as in the tsv just maps barcodes to samples but you do not have a separate barcode sequence file? choose your own adventure: Where are your barcodes? in-line with the sequences a. see the q2-cutadapt tutorial in the header line or some place else a. :sob: QIIME 2 does not have a way to handle …

Hi @msport469 and @Nicholas_Bokulich , I'm working with some data that was similarly processed. After some searching, I found on Biostars a package BBMap , available from bioconda , that comes with a script demuxbyname.sh that will do what we want. If your fastq header looks like this (with barcode o…

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