The original trace data from which the readings where derived can be seen by double clicking (two quick clicks) with the middle mouse button on the area of interest. 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 instead of a reading displays up to four readings overlapping that point. Double clicking on a reading which already has the trace displayed will cause the cursor in the appropriate trace display to quickly grow and shrink to act as a easy visual way to identify which trace is which.
Note that the files containing the traces must either be in the directory from which gap4 was started or in directories defined by the environment variable RAWDATA. For example if the trace files for a project were in /pubseq/pubseq/mydata/traces and /fred/freds_traces then before starting gap4 define RAWDATA as follows:
csh% setenv RAWDATA /pubseq/pubseq/mydata/traces:/fred/freds_traces (or) sh$ RAWDATA=/pubseq/pubseq/mydata/traces:/fred/freds_traces; export RAWDATA
The picture shows an example of two displayed traces. On the left is
the name of the reading and two buttons to display information and
quit. Pressing the info button will bring up the window displayed in
the bottom right of the picture. It will contain the comments from the
readings' SCF file. Between these buttons and the trace
display itself are two vertical scale bars. Moving these will zoom the
traces in the X or Y direction. The default Y scale is to fit the highest
peak on the screen without clipping.
The trace is displayed on the right with a scrollbar
directly above it. The vertical line seen in these two 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
scrolling of the trace windows and vice versa.
The trace display can now (1999) display any number of traces at once,
although by default a scrollbar will be needed to view more than five at once.
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.
The
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
(any other button cancels the operation) anywhere on another trace that has a
"Diff" button will create the difference trace. The algorithm used for
computing the difference trace is adjustable by parameters in the settings
menu (see section Trace Display Settings).
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.
![[picture]](contig_editor.traces.gif.html)
(Click for full size image)
set_def TRACE_DISPLAY.NUM_TRACES 5
set_def TRACE_DISPLAY.TRACE_HEIGHT 150
set_def TRACE_DISPLAY.DIRECTION bottom
TRACE_DISPLAY.DIRECTION may be used to control where new traces get
added. By default this is to the bottom of the window, however setting this to
top will make sure that new traces appear at the top of the trace
window.
This page is maintained by
James Bonfield.
Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_60.html