2. Example Amplicon Project Design and Analysis
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2.6 Other Issues of Special Interest
: 2.6.2 How Should Your Project Be Organized?
2.6.2
How Should Your Project Be Organized?
Once you have decided on your preferred definition of ‘Sample’, you need to decide how your Samples and Amplicons should be organized within one or more Projects. Projects should be used to group together analyses for either ease of comparison or ease of navigation.
Much of the effort in setting up a Project has to do with defining Reference Sequences and Amplicons. Therefore, it is advisable to set up your Projects so that they contain Amplicons that will be measured across a variety of Samples. That way you can continue to add new Samples to the existing Project rather than starting a new Project for each batch of Samples.
In the case where you are scanning for a large number of different Amplicons from a single data source, collecting them within the same Project would also make sense because it would make navigation easier. It would eliminate unnecessary additional navigation clicks to open individual Projects when trying to jump from Amplicon to Amplicon during a review of your results.
You are free to organize your Sample-Amplicon analyses into one or more Projects as you find convenient. If you are a low volume user, you may be tempted to keep all of your analyses in the same Project even if they are unrelated to each other. However, you should keep in mind that pooling too many unrelated Samples together in a Project may unnecessarily clutter navigation menus and Variant summary pages.
