How to import multiplexed data?

[chiara (Chiara Conte)]

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,
Chiara

[thermokarst]

Hi @chiara!

@chiara

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.

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!