I would like to know if there is a straightforward way to see what percent of my reads could not be demultiplexed. I am looking for this information because I am getting fewer than expected reads per sample, and I want to check whether this is because many of my reads could not be demultiplexed.
Here is my demux command:
qiime demux emp-paired \ --i-seqs qiime2_output/sequences.qza \ --m-barcodes-file sample_metadata.txt \ --m-barcodes-column BarcodeSequence \ --o-per-sample-sequences qiime2_output/demux.qza \ --o-error-correction-details qiime2_output/demux-details.qza \ --p-rev-comp-mapping-barcodes
Attempt #1: I tried adding
--verbose, but I don't think this created any new information in my logs.
Attempt #2: I thought this information might be in
demux-details.qza, so I tried converting it to a .qzv file with the following command:
qiime metadata tabulate \ --m-input-file qiime2_output/demux-details.qza \ --o-visualization qiime2_output/demux-details.qzv
I was only able to make this command work after allocating >16 GB of RAM, and I couldn't open it in the online QIIME2 viewer. The file is 743 Mb, so maybe it's too big? (N.B. I see that you are working on improving this command, and I think that would be great.)
My question is: Is this the right way to find the information I'm looking for? I feel like it would be extremely useful to show this number (% reads that couldn't be demultiplexed) in the output of
P.S. I am using QIIME version 2021.2.0, which I installed with conda.