In demultiplexing step in the Qiime2 tutorial https://docs.qiime2.org/2019.1/tutorials/atacama-soils/#atacama-demux it is said that a user has to have a barcode file with fastq.gz extension. I do not have barcode with this file extension (I know the barcod’s sequences used in my amplicons). Do I have to make it manually? If so, how? By Qiime2 or what? or how can I provide it?
Next question: After having the three files R, F and barcode, should they be put in a directory? Then run this command below:
qiime tools import _
_ --type EMPPairedEndSequences _
_ --input-path emp-paired-end-sequences _
_ --output-path emp-paired-end-sequences.qza
If yes, I opened this command’s view there is written:
But there is no FORMAT argument in the command mentioned.
Another question: this step highly looks like the importing step. Why we do this part of demultiplexing? Othwerise, it is already done in the previous step!
and finally, in the main demultiplexing command, there is an argument with .tsv extension. For my data, how can I provide it? This format is used in the next steps, not in the earlier steps based on what I read in the tutorial.