'Multiplexed paired-end FASTQ with barcodes in sequence' vs 'Fastq Manifest' format?


I have to import a multiplexed paired-end fastq.gz file and am not sure which method to use? Since there is no separate barcode file I usually would demultiplex my data separately before running it through the manifest pipeline but with the latest qiime2 update there is a new option of importing for Multiplexed paired-end FASTQ with barcodes in sequence. Not sure how this is different from using the Manifest format? I did read up on it at Importing data — QIIME 2 2021.2.0 documentation but didn’t quite get the difference


Hi @Samrin_Shaikh,
I am not sure I understand your question but I am going to try to answer and let me know if I don’t answer your question and I will try again!

So from what I understand you are wondering what the difference between Manifest format and Multiplexed paired-end FASTQ with barcodes in sequence?

A general overview is:
They are similar in the fact that they are both ways of importing multiplexed data.
They are different in the fact the Manifest format doesn’t include barcodes in the sequences while Multiplexed paired-end FASTQ with barcodes in sequence does.

If you want more specifics about what you need to run these commands, I would point you back to the
importing data tutorial that you linked. That has very detailed instructions on what you need for/how to run the command.

I hope that helps
Chloe :turtle:

Thank you @cherman2 . I was confused about which method to use for importing my data. All cleared up now :slightly_smiling_face:

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