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Reading and Template Plot

The main section of the template display is the large upper plot showing the templates and readings. Colour is used to illustrate information pertaining to the templates and readings. The reading colour is used to convey the primer information. The default colours are:

red
primer unknown
cyan
forwards primer
grey
reverse primer
dark cyan
custom forward primer
dark grey
custom reverse primer

For the templates, the colour is used to distinguish the number and location of readings sequenced from this template. Templates with readings sequenced from only one end of the template are drawn in blue. Those with readings sequenced from both ends are pink when both ends are contained within the contig and green when the ends are in different contigs.

For each template Gap stores an expected length, as a range between two values. From an assembly it is often possible to work out the actual length of a template based upon the positions within a contig of readings sequenced using the forward and reverse primers. If this observed distance is outside of the range of acceptable sizes then the template is drawn in black. Alternatively it may be possible that both forward and reverse readings are assembled on the same strand (in which case both arrows will point in the same direction). This too is a problem and hence the templates are drawn in black.

If more than one contig is displayed then the distance between adjacent contigs is determined from any read pair information. If there are spanning templates between two adjacent contigs and the readings on that template are consistent ie are in the correct orientation, the template is coloured yellow. Templates which span non-adjacent contigs in the display or contain inconsistent readings are coloured dark yellow.

A summary of the default template colours follows.

blue
the template contains only readings from one end
pink
the template contains both forward and reverse readings within this contig
green
the template contains both forward and reverse readings, but they are in separate contigs
black
the readings on the template are within the same contig but are in contradictory orientations or are an unexpected distance apart
yellow
the readings on the template are within different contigs and are consistent
dark yellow
the readings on the template are within different contigs and are inconsistent

Within the figure the contents of the View menu are visible. The "Ruler", "Templates", "Readings", "Quality Plot" and "Restriction Enzyme Plot" commands control which attributes to display. 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 file as NUM_TICKS although the actual number of ticks per contig that will be displayed depends on the pixel length of the contig and the production of suitable tick numbers.

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 plot can be enlarged or reduced using the standard zooming mechanism (control right mouse button). The "zoom out" button redraws the display at the previous zoom level. 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.

The contig editor can be invoked by double clicking on the middle mouse button in any of the displays, ie template, ruler, quality or restriction enzyme plots. The editor will start up with the editing cursor on the base that corresponds to the position clicked on in the template display. If more than one contig is currently being displayed the editor decides which contig to show using the following rules. If the user clicks on the quality plot, the contig lines or the restriction enzyme display, the corresponding contigs will be shown. If the user clicks on a gap between these displays the nearest contig will be selected. If the user clicks on the template or reading lines, the editor will show the contig whose left end is both to the left of and closest to the cursor.

The blue vertical line seen to the left of figure is the position of the editing cursor within a contig editor. Each editor will produce its own cursor so several may be visible at a time. Moving the editing cursor within a contig editor automatically moves its cursor within the template display. Similarly, clicking and dragging the editor cursor with the middle mouse button within the template display scrolls the associated contig editor.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_76.html