I’m trying to determine the adequate cutoff value for trimming my reads. I want to select this value in a way more objective than squinting at the boxplot in the visualization artifact, and I’d like to access the raw data used to create this plot so I can play with it. Is it possible to fetch this data from the .qzv file?
Hi @jacodela! This sounds like a great idea — I opened up an issue on our issue tracker to put this on our radar! Unfortunately, I don’t have a good alternative or workaround for you at the moment. The data is technically available in your QZV file, but it is formatted as a JSONP file, which depending on your comfort level could be a pain to work with.
In the meantime, I think the
summarize interactive quality plot is your best bet. Just in case it isn’t clear, you can zoom in on regions of interest in that viz by clicking and dragging (and you can zoom back out by double-clicking).
Keep us posted! We will update this thread when this feature is available (I don’t have an ETA at present).
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This is now possible by downloading a CSV of 7-number summaries in QIIME 2 2018.2 thanks to contributions by @mahermassoud!