How to import multiplexed data?

Hi @thermokarst,
I have read your conversation with Yuhe and I am actually facing the same doubt, due to the fact that I am new to informatics stuff and I am still learning Qiime2, so I apologize whether my question sounds silly.
My data are multiplexed and joined with the barcode and they are gathered just in one file.
Hence, I do not know how to make my manifest fastq file as the absolute file-path for each sample and every direction would be exactly the same.
Would it be right to make a PairedEndFastqManifestPhred33?
Should I use the following command then?
qiime tools import
–type PairedEndFastqManifestPhred33\
–input-path Mymanifestfile
–output-path myartifact.qza

I hope it was clear enough.

Thanks for your kind attention and your help.
Best regards,

Hi @chiara!

Since your data is still multiplexed, the manifest format is not applicable to you (those are only for demultiplexed reads).

Sounds like you have a perfect use case for importing your multiplexed reads and demultiplexing using the q2-cutadapt plugin! Check out this community tutorial for some more information:

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

Take some time to look at that document, and if you get stuck, come find us here for help!

Good luck! :t_rex:

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