How to review the sequences in the demux-paired-end data?

Continuing the discussion from Next steps following Importing demultiplexed sequences data in Casava format:

@ebolyen That should be possible, you will just need to import your data as SampleData[SequencesWithQuality], I would check out the importing tutorial and if you have any further questions on that, please feel free to create a new topic on the forum!

The question is that all our data are demux paired-end, I used the Casava 1.8 paired-end demultiplexed fastq, which created the demux-paired-end.qza. Then, by starting the tutorial with demux-paired-end.qza, how can I can run the qiime demux summarize --i-data demux.qza --o-visualization demux.qzv to review the summary of these sequences?


You can just pass demux-paired-end.qza to the --i-data parameter of qiime demux summarize.

The filenames aren’t important at all, what matters is the type, which you can use qiime tools peek /path/to/something.qza to see.

You’ll notice that your paired-end artifact has the type of SampleData[PairedEndSequencesWithQuality] and the type expected for --i-data is SampleData[PairedEndSequencesWithQuality | SequencesWithQuality] (you can see that by running qiime demux summarize --help), which means sample-data of either paired end sequences (fastq) or single end (fastq) is valid input for the --i-data parameter of qiime demux summarize.

This process holds true for everything in QIIME 2, so if you are ever unsure what something needs, you can just use --help and qiime tools peek to see what is needed, and what you have on hand.