Hi everyone! I am using qiime2-2021.4 on a conda environment. We use FASTQ files generated from a 16S run on the Illumina MiSeq as our initial input in QIIME2.
Lately we've been having an issue and I am trying to narrow down whether it is an instrument issue or a QIIME2 issue, though I tend to lean towards instrument. Nonetheless, I figured I would check.
Basically after demultiplexing (even with a file that has ~200 MBP of data generated, which is our normal file size that would generate a forward sequence count of perhaps ~20k reads per sample), we are only seeing a forward sequence count of around ~300 per sample and we have absolutely no idea why.
Here is the code that we are running:
qiime tools import
qiime demux emp-single
qiime demux summarize
qiime tools view demultiplexed.qzv
Is there a possibility that this is a QIIME2 issue? Again, inclined to think it is not but just want to cover my bases.