I am attempting to demultiplex my data with demux but I am unsure how to have this command read my files properly. My sequences are in .fastq format and my mapping file is just a .txt and looks like this:
Thanks for reaching out, apologies for the delay in response here!
I'd recommend checking out our User Docs to learn about how to import your data into QIIME 2 - this will walk you through how to import your data based on the format of your sequences. Once you've done that, you can take a look at the documentation on our demux commands and which one makes the most sense for your data.