I am using qiime 1.9.1 but in parallel, I am trying to move to qiime2 with the AWS installing option.
I saw the sheet that compares qiime 1 and qiime2 scripts (please, you can find the link below) https://docs.google.com/spreadsheets/d/1AOyA84lGPBk5C2Uflg_pILEL75a6_gdY6SK3ltOt44E/pubhtml?gid=0&single=true
My question is if the NA scripts from qiime1 would work in a qiime2 environment as I would like to make sure that I can run the full analyses before I pay the AWS plan.
Thank you very much for your kind attention and I apologise for my basic questions.
Really good question.
First of, check the notes in each of the commands, even if it’s says NA, there could be an option in QIIME2 to perform that operation but perhaps not as a single script but as a plugin.
Now, when you start the AWS QIIME2 machine, it will only have QIIME2, which was installed via conda. One of the really cool things about environment managers, like conda, is that they will allow you to have multiple version of the same code installed without conflict. Thus, you will be able to install qiime 1.9.1 by following these instructions. After that you will be able to switch between environments and QIIME versions. BTW, you could test this in a local machine by following the install instructions of QIIME and QIIME2.
Finally, note that most analyses on the feature tables will run pretty fast in an OK/newish computer AKA you might not need to run all your analyses in AWS.
Hope this helps!
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