I am very new to Qiime2 and I successfully imported my sequence data via paired-end fastqmanifestphred33 format. I think I am getting confused on the step to take after this importing step. I was able to run through the moving pictures tutorial with the sample data however applying my own data to those commands is tripping me up. The sequences are already demultiplexed so I tried skipping over that step in the tutorial to generate a feature table but found that to not work. I then tried running the demultiplexing step anyway for paired-end sequences in the Atacama soil tutorial and the error below popped up. This is leading me to think that my sequences were merged incorrectly into qiime2 so I am a little lost on what step to take.
Sorry for the long question, I just need a very basic answer on if my import worked and then the next step to take after I received a paired-end-demux.qza output
Plugin error from demux:
** Argument to input ‘seqs’ is not a subtype of EMPPairedEndSequences.**
Debug info has been saved to /var/folders/m6/kby0dlrd3cz8gsrdfqchxg680000gn/T/qiime2-q2cli-err-vpa94vfb.log.
Your manifest file is the CSV you specified during your import step, so judging from the command you just provided, that filename is called RC16s.csv. You can attach that file, or paste just the first 5-10 lines of the file’s contents.
Since your data is already demultiplexed, the next step you should take after importing is to proceed straight to quality control, using either q2-dada2 or q2-deblur! Using q2-dada2, you would pick up in the Atacama tutorial here, specifically at the qiime demux summarize step. You will need to specify the filename of your demultiplexed sequences in the summarize command, so it will look something like this: