Hey! I konw this question is too old but I’d like to know if there is an option avaialable these days for this "dual-indexing " in the demultiplexing
Qiime 2 does not support dual-index reads, according to the documentation.
But it does suggest another option!
So for the time being, this type of demultiplexing needs to be done outside of QIIME 2 using other tools, for example bcl2fastq.
Let me know if that works for you.
P.S. Github issue cross ref for #55 q2-demux
In order to continue with the topic in the forum… Colin… you say… it is allowed to do the dual demultiplexing in QIIME 1 and then continue with QIIME 2 ???
Yes, yes you could!
After demultiplexing and quality filtering with Qiime 1, you will have a
seqs.fna file with qiime labels. You can them import that
seqs.fna file into a Qiime 2
Let me know if this method works for you!
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