I am running Qiime2 2019.7 in a Conda environment. I am working with data which I got back demultiplexed from an Illumina miseq 2x300 kit.
My dataset is comprised of 279 samples + 1 sample that is “undefined” which I believe consists of all the reads which Illumina couldn’t properly demultiplex. I have two undefined fastq’s (F and R), so I know this is an issue from the actual Illumina software, but I thought that someone here might be able to direct me to some useful information. In particular I am wondering the following.
What causes a read to be undefined? Is this an issue with the barcode getting messed up during the demultiplexing process?
Is there any way to salvage even some of these reads? I’m including my demux.qzv and my table.qzv to show just how many reads are showing up as undefined. It is my single biggest sample, which is a little depressing.
Again, I realize that half of this issue is outside of QIIME2, but if anyone has any information I would be extremely appreciative!
Illumina-demux.qzv (313.4 KB)
table.qzv (1003.4 KB)