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Reference traces

From the "settings" menu of the editor the trace display can be set to "Auto-Diff traces". Once this is activated, whenever the user double clicks on a base in the editor sequence display, not only is the reading's trace displayed, but also its designated reference trace plus the difference between them. If its complementary reading is available, its trace and reference trace and their differences are also displayed.

The preferred way of assigning reference traces to readings is by use of "naming conventions"; that is to have a simple set of rules which control the names given to the trace files. It can be seen in the figures showing the editor that forward and reverse readings from the same patient have names with a common root but which end either F or R. This both ties the two together (so the software knows which is the corresponding complementary trace when the user double clicks on a reading) and also enables the association of readings and their reference traces. Once a convention has been adopted the rules can be defined for pregap4 by loading them via the "Load Naming Scheme" option in its File menu (see section Pregap4 Naming Schemes). For any batch of readings the reference traces are defined within pregap4's "Reference Traces" module.

Within the Contig Editor reference traces can be set by right clicking on their names in the editor. When this is done a menu will popup. This allows the user to select whether the trace is to be used as a positive or negative control.

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This page is maintained by staden-package. Last generated on 22 October 2002.