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
I hope it was clear enough.
Thanks for your kind attention and your help.