Demultiplex raw data from Qiita in Qiime2


I am trying to demultiplex raw data downloaded as seqs.fastq.qz (preprocessed fastq) from Qiita. I followed the "Moving Picture" tutorial which required me to import the data first.

Because my data was in “EMP protocol” multiplexed paired-end fastq format, I was directed to "Importing data" help page and it says that I need three files: forward.fastq.gz, reverse,fastq.gz, barcodes.fastq.gz. However, it seems like, in my case, the barcode, forward sequences and reverse sequences are all in one seq.fastq.gz file. I wonder how I could separate them into three individual file?

Thank you very much~

Hi @syt_00,

Thanks for reaching out, and welcome to the :qiime2: forum!

Can you please try running the following command for me, and let me know if you are successful?

qiime tools import \
  --type MultiplexedPairedEndBarcodeInSequence \
  --input-path seq.fastq.gz \
  --output-path multiplexed-seqs.qza

If not, please copy/paste the error message you receive in your terminal. Thanks! :lizard:

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