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Traces

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

[picture]
(Click for full size image)

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.

set_def TRACE_DISPLAY.NUM_TRACES	5
set_def TRACE_DISPLAY.TRACE_HEIGHT	150
set_def TRACE_DISPLAY.DIRECTION		bottom

The 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.

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.


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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_60.html