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Reading and Template Plot Options

(Click for full size image)

Within the figure shown above the contents of the View menu are visible. The "Templates", "Readings", "Quality Plot" and "Restriction Enzyme Plot" commands control which attributes are displayed. The graphics are always scaled to fit the information within the window size, subject to the current zoom level. This means that turning off templates, but leaving readings displayed, will improve visibility of the reading information.

The "Ruler ticks" checkbox determines whether to draw numerical ticks on the contigs. The number of ticks is defined in the .gaprc (see section Options Menu) file as NUM_TICKS although the actual number of ticks per contig that will be displayed also depends on the space available on the screen.

The "ignore 'single' templates" toggle controls whether to display all templates or only those containing more than one reading. The "show only read pairs" toggle controls whether all templates or only those containing both forward and reverse readings are displayed. Hence when set the templates displayed are those with a known (observed) length. The "Show only spanning read pairs" toggle controls whether to display all templates or only those containing forward and reverse readings which are in different contigs.

The plot can be enlarged or reduced using the standard zooming mechanism.See section Zooming.

The crosshair toggle button controls whether the cursor is visible. This is shown as a black vertical line. The position of the crosshair is displayed in the two boxes to the right of the crosshair toggle. The first box indicates the cursor position in the current contig. The second box indicates the overall position of the cursor in the consensus. The third box is used to show the distance between restriction enzyme cut sites. See section Restriction Enzyme Plot.

Tags that are on the consensus can only be seen on the ruler. These are marked beneath the ruler line. Tags on readings can be seen both on the ruler (above the line) and on their appropriate readings within the template window. To configure the tag types that are shown use the "select Tags" command in the View menu. This brings up the usual tag selection dialog box. See section Tag Selector.

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