Really appreciate your help. The command works well now.
Can I ask another question regarding the function of "qiime cutadapt demux-paired"? There is no argument like "--p-rev-comp-barcodes" or "--p-rev-comp-mapping-barcodes". I'm wondering whether it would reverse and complement the barcodes during demultiplexing?
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Hi @Claire010!
cutadapt (the tool that q2-cutadapt is wrapping) is like a simple "find and replace" search in a word processor - you tell it what to find (your barcodes), and it replaces the barcode with nothing (effectively removing (or cutting) that subsequence from the read). In the process, it copies the trimmed read into a new sample file that that barcode was mapped to.
So at the end of the day, you need to search for the barcodes in the sequence in whatever orientation that might be in. If the barcodes need to be reverse complemented, you'll need to do that separately, before running this command.
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