I’ve been trying to analyze paired-end reads with the community AMI and it looks like
denoise-paired command no longer exists and all the documentation pages using it warn that they are old. What would be the next step to use dada2 after I have the demux.qza artifact?
denoise-paired does still exist. It’s available in QIIME 2 2017.2 and 2017.4, but not earlier versions. You can always see the available plugins and methods on the QIIME 2 plugins page (here for version 2017.4.
You should confirm that you’re using one of these two versions of QIIME 2 by calling
qiime info. It’s possible that you booted an older AMI which does not have the
@akknight216: Just curious — did you find the documentation pages via a Google/Bing/Yahoo search? If so, it does look like those major search engines have cached old versions of our documentation. For now your best bet is to visit https://docs.qiime2.org directly and use the built-in search (we know that search isn’t the best, but it guarantees up-to-date docs). Visiting the docs site directly should always load the latest version of the docs, and if you want to view older versions, use the selector on the left (see this post for details). We are considering our options for handling search engine optimization for future releases of QIIME 2. Thanks!
Yes, I did-it seems that the older pages come up first for google. I did eventually find the right pages. Thanks!
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