Hi to the community!
I wanted to ask wheter there is somebody that performed demultiplexing through QIIME2 of dual indexed reads (tagF----read-----tagR). I tried to look for it in the forum of course, finding situations apparently similar to mine, but without understanding with clarity how to cope with this problem.
I hope this is not a redundant post, and that someone may help.
Thanks for the attention
We work with dual index reads.
I use cutadapt to demultiplex as described here (User guide — Cutadapt 3.7 documentation). Look for Demultiplexing paired-end reads with combinatorial dual indexes. Then import into qiime2 using manifest file.