The original trace data from which the readings where derived can be displayed by double clicking (two quick clicks) with the left or middle mouse button on the area of interest. Control t has the same effect. The trace will be displayed centred around the base clicked upon and the name of the reading in the contig editor will be highlighted. Double clicking on the consensus displays all the readings covering that position. Double clicking on a reading which already has its trace displayed will cause the corresponding trace to be surrounded by a red border.
Moving the mouse pointer over a base causes the display of an information line at the bottom of the window. This gives the base type, its position in the sequence, and its confidence value.
There are two forms of trace display which are selected using the "Compact" button at the top of the Trace display. The compact form differs by not showing the Info, Diff, Comp. and Cancel buttons at the left of each trace.
Note that gap4 does not store the trace files in the project database: it stores only their names and reads them when required. However it does not know which directory they are stored in, unless this is specified using the "Trace File Location" option (see section Trace File Location).
The picture shows an example of three displayed traces. The reading number,
together with the direction of the reading (+ or -) and the chemistry by
which it was determined, is given at the top left of each sub window.
The chemistry information is found from comments in the experiment file.
'uf' and 'ur' indicate universal forward and universal reverse, 'cf' and 'cf'
indicate custom forward and custom reverse, and 'p' and 't' indicate primer
and terminator. There are four buttons ('Info', 'Diff', 'Comp.' and 'Cancel')
below this information, and X and Y scale bars to the right.
The "Info" button will display a window like the one shown at the bottom right
of the picture. This contains the comments from the relevant SCF file.
The "Diff" buttons are used to produce a new trace showing the differences
between two existing traces. To use this, press "Diff" in any window. The
mouse cursor then changes to a cross symbol. Pressing the left mouse button
anywhere on another trace that has a "Diff" button will create the difference
trace. Any other button cancels the operation. The algorithm used for
computing the difference trace is adjustable by parameters in the settings
menu (see section Trace Display Settings).
The trace differencing was originally designed for visual inspection of
suspected mutations
Bonfield, J.K., Rada, C. and Staden, R. Automated detection of point
mutations using fluorescent sequence trace subtraction. Nucleic Acids Res. 26,
3404-3409 (1998).
The "Comp." button complements the displayed trace. If the sequence in the
editor has been complemented then the trace will automatically be shown in the
complementary sense. This button may be used to toggle the complementarity.
The "Cancel" button will remove the trace.
The X and Y scale bars zoom the trace in the appropriate direction. The default
Y scale is to fit the highest peak on the screen without clipping. When the
"Show confidence" check-button is selected, the confidence value for each base
call will be displayed as a histogram, overlayed on the trace displays. The
base confidence values are not computed by gap4, but rather are read from the
SCF file which is assumed to have been generated by one of the programs that
compute confidence values (such as phred, ATQA or eba). When ABI files are in
use, confidence values may not be shown.
The trace is displayed on the right with a scrollbar directly below it and
with the reading name in the top left corner. The vertical line seen in these
three traces shows the location of the editing cursor in the contig editor window.
The lock button on the trace displays ties the editing cursor movement to the
scrolling of the trace windows and vice versa.
The trace display supports the display of up to four columns of traces,
and can display any number of rows. The number of columns and rows can
be configured and saved using the buttons at the top of the window. A
scrollbar is provided if there are more traces to display than can be
viewed with the current settings.
To modify the number of traces that are shown at any one time, and the heights
of these, add (and edit) the following lines to your `$HOME/.gaprc' file.
New traces are always added to the bottom right of the window.
Resizing the width of the trace window, moving the trace window and
adjusting the X magnification are all remembered and used when bringing
up new trace displays.
The "Close" button at the top right of the Trace Display removes the
Trace Display.
An example of the "Compact" form of the trace display is shown below.
![[picture]](contig_editor.traces.unix.gif.html)
(Click for full size image)
set_def TRACE_DISPLAY.ROWS 5
set_def TRACE_DISPLAY.COLUMNS 2
set_def TRACE_DISPLAY.TRACE_HEIGHT 150
![[picture]](contig_editor.traces.compact.unix.gif.html)
(Click for full size image)
This page is maintained by
staden-package.
Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_62.html