Populating the Global Align Tab

1.6.1

When you open an Amplicon Project in the AVA software, the Global Align tab has no content and is grayed-out. To populate it from this state, you must use a right-click “Global Align” action from one of the following two sources:

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A Sample-Amplicon pair, from any of the 3 Project Tree views, on the Project Tab [see sections 1.3.1.1, 1.3.1.2, and 1.3.1.3; note that the Amplicon must be fully defined (section 1.3.2.2) and the computation must have been carried out (section 1.4)]. Right-clicking on a Sample (in the References Tree) or an Amplicon (in the Read Data Tree or the Samples Tree) opens a contextual menu that includes a “Global Align” option; choosing this will populate the Global Align tab with the multi-alignment of the reads for the Sample-Amplicon pair on that branch of the tree.

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A Sample-Variant pair, from the Variants Table, on the Variants tab [see section 1.5.1.3; note that the Variant must be fully defined (section 1.3.2.5) and the computation must have been carried out (section 1.4)]. Right-clicking on an appropriate cell of the Variants Table opens a contextual menu that includes a “Global Align” option; choosing this will populate the Global Align tab with the multi-alignment of the reads of all the Amplicons that cover this Variant on the Reference Sequence and that are associated with this Sample.

Once the Global Align tab is populated, you can still use the right-click method above, and replace the multi-alignment displayed with another one. But from inside the Global Align tab, you have another, more powerful option: this tab has two “Alignment data” controls in its upper-left corner that allow you to browse through and navigate all the alignments of your Project without leaving this tab, and even to view the data for multiple Amplicons together (for a given Sample-Reference Sequence pair). These controls are described in detail in section 1.6.4.1.