2. Example Amplicon Project Design and Analysis
: 2.6 Other Issues of Special Interest
2.6
Other Issues of Special Interest
2.6.1 What Does ‘Sample’ Mean?
2.6.2 How Should Your Project Be Organized?
2.6.3 Should Amplicons Share a Reference Sequence or Have Individual Ones?
2.6.4 When should MIDs be used?
2.6.5 What is the purpose of Multiplexers?
When you are familiar with the basics of the ‘Amplicon Variant Analysis’ software and you are ready to setup projects with your own data, you should take some time to consider the optimum setup for your project given the specifics of your experimental design and the way in which you intend to analyze the results. Primarily, you need to decide what the term ‘Sample’ means to you; you need to decide what type of project organization you need; and you need to decide on the relationships between your Amplicons and Reference Sequences.
