The purpose of this menu is to configure the operation of the contig editor, including the consensus calculation, the active tags and the status lines. Settings for the following options can be changed.
The contig editor can display several additional text lines underneath the consensus sequence. These are of textual format and provide additional information about the data displayed above. Currently, there are two forms of status line available. These are "Strands" and "Translate Frame". Both status line types update automatically as edits are made that change the consensus.
The status line menu is accessed by cascading off the settings menu. It contains the following.
"Show Strands" creates a single line consisting of the +, -, = and ! characters. These stand for positive strand only, negative strand only, both strands (in agreement) and both strands (in disagreement) respectively.
The frame translation status lines provide translations in each of the six available reading frames. This data can be displayed in either the single character or the three character amino acid codes.
Pressing the right mouse button on the 'name' segment of the status line (on the left hand side) pops up a menu. The commands available may depend on the type of the status line chosen, however currently it will always only contain the "Remove" command. This, as expected, removes the status line from the display. To remove all status lines use the "Remove all" command from the "Status Line" cascading menu.
The data in the status line may neither be cut and pasted, modified or searched; it is not possible to move the cursor into these lines.
The editor trace display has a number of configurations specific to its own usage. The "Trace Display" cascading menu of the "Settings" menu contains these configurations. They are as follows.
When switched on, auto-display traces will direct certain searches to
automatically display relevant traces to aid in solving the problem. This
works in conjunction with most appropriate searches. The traces chosen to
solve the "problem" will, by default, be the best trace from each strand which
agrees with the consensus (which is calculated at 1% consensus cutoff) and the
best trace from each strand which disagrees with the consensus. This selection
of traces may be adjusted by modifying the
CONTIG_EDITOR.AUTO_DISPLAY_TRACES_CONF configuration variable. The
default setting of this is "
+ - +d -d". Each of the space separated
elements in this string corresponds to a trace file to choose. If one cannot
be found, then it is ignored. The order listed here is the order in which they
will be displayed in the trace window. The complete list of available trace
The "normal mode", "diff against consensus trace", and "diff against specific trace" control the operation of bringing up an individual trace, which for documentation purposes we shall term the "chosen trace". Only one of these three options can be enabled at any one time. In "normal mode", the chosen trace is simply displayed and no more automatic operations are performed. When either of the other two modes are used, the chosen trace is displayed along with either the consensus trace or a specified trace (which is chosen when selecting the "specific trace" mode). A third trace plots the differences between the chosen trace and the second trace.
The consensus trace, when shown, is computed as the average of the other traces of the same orientation overlapping the region of the consensus that the chosen trace covers. With "only matching reads" set, the consensus trace at each base is computed as the average of the reads that have the same base call, otherwise all traces of the correct orientation are used. If "ignore selected read" is set, the chosen trace itself is not used in the consensus trace calculation.
The "difference" trace is calculated by subtracting the two traces using an algorithm determined by the "show positive differences" and "Y scale differences" options. "Show positive differences" displays the absolute difference values. For example, subtracting a large "A" peak from a "C" peak would show both "A" and a "C" difference peaks rising upwards from the bottom of the trace window. With "show positive differences" disabled, the base line (meaning zero differences) is in the centre of the trace and one peak will be above this base line and the other beneath it. The "Y scale differences" option controls the scaling of trace values prior to subtraction. When disabled, the raw differences between trace values are shown. When set, the two traces are normalised such that the total signal strength (defined as the sum of the four trace levels at each point) for each trace is identical.
For further information about mutation detection, seesection Search for Mutations.
This toggles between the normal sequence display showing the current base assignments and one in which those assignments that differ from the consensus are clearly highlighted. This makes scanning for problems by eye much easier.
Several modes of highlighting are available. "By dots" will only display the bases that differ with the consensus, displaying all other bases as full stops. The base colours are as normal (ie reflecting tags and quality). "By foreground colour" and "By background colour" displays all base characters, but colours those that differ from the consensus. This allows easier visual scanning of the context that a difference occurs in, but it may be wise to disable the displaying of tags. Finally the "Case sensitive" toggle controls whether upper and lower case bases of the same base type should be considered differences.
This toggles the consensus calculation routine between treating both strands together or independently. In the independent case any difference between the two strands is shown in the consensus as a '-'. Hence these clashes are found as problems by the "Search by problem" code.
Selecting auto-save toggles the auto save feature. Initially this is turned off each time the contig editor is invoked. Once toggled the adjacent checkbox will be set to indicate the feature is enabled and the contig will be saved. From that point onwards the contig editor will write its data to disk every 50 edits. Each time an auto save is performed notice is given in the output window. Saving more frequently can still be performed manually by using "Save Contig".
The "Undo" button will allow the user to undo edits regardless of when the last auto save occurred. Note that the same is not true regarding the manual "Save Contig" method.
The codon translation within the status line by default displays single character amino acid codes. Selecting the "3 Character Amino Acids" setting will toggle the status line to display three character amino acid codes.
When set, this forces readings from the same template to be displayed vertically adjacent to one another. The real "X coordinate" of the reading is not changed, so this has no effect for readings from the same template that are never visible together on the screen at the same time. The purpose of the function is to group batches of readings together. Note that at present when using this option the operation of the up and down arrow keys incorrectly affects the editing cursor. Using the mouse to position the editing cursor still works correctly.
This option may be useful when a rigid sequencing practise is in use where the same clone is always sequences several times (possibly once from each end) and where these sequences overlap. In such cases it could be useful to make sure that the sequences from the same clone are adjacent to one another in the editor.
When the quality cutoff value is 0 or higher and the either of the show reading quality and show consensus quality toggles are set, the background for bases is shaded in a grey level dependent on the quality. There are ten levels of shading with the darkest representing poor data and the lightest representing good data. So with the quality cutoff set to 50, all bases with a quality of less than fifty are shown with a red foreground and a dark grey background, bases with quality just above 50 will have the darkest grey background, and bases with a quality of 100 will have the lightest background. When tags are present the background colour is that of the tag rather than the quality.
The colours used are adjustable by modifying your `.gaprc' file. The defaults follow.
set_def CONTIG_EDITOR.QUAL0_COLOUR "#494949" set_def CONTIG_EDITOR.QUAL1_COLOUR "#696969" set_def CONTIG_EDITOR.QUAL2_COLOUR "#898989" set_def CONTIG_EDITOR.QUAL3_COLOUR "#a9a9a9" set_def CONTIG_EDITOR.QUAL4_COLOUR "#b9b9b9" set_def CONTIG_EDITOR.QUAL5_COLOUR "#c9c9c9" set_def CONTIG_EDITOR.QUAL6_COLOUR "#d9d9d9" set_def CONTIG_EDITOR.QUAL7_COLOUR "#e0e0e0" set_def CONTIG_EDITOR.QUAL8_COLOUR "#e8e8e8" set_def CONTIG_EDITOR.QUAL9_COLOUR "#f0f0f0" set_def CONTIG_EDITOR.QUAL_IGNORE "#ff5050"
When set, any change between the sequence displayed and the original sequence held in the trace files is shown by changing the background colour of the appropriate base. The detection of these edits depends on the quality values and the "original position" data. Hence the traces do not need to be present in order to detect edits. The colour of the bases reflects the type of change found. The colours are adjustable by editing the `.gaprc' file. The following table lists the colour, gaprc variable and the meaning.
CONTIG_EDITOR.EDIT_BASE_COLOUR-- Base change or insertion
CONTIG_EDITOR.EDIT_PAD_COLOUR-- Padding character
CONTIG_EDITOR.EDIT_CONF_COLOUR-- Confidence value
"Set Active Tags" allows configuration of which tag types should be displayed within the editor. Note that searches for tag annotations will only examine active tags, but searching for a specific tag type will find tags even when tags of this type are not visible. In this situation the tag will still be invisible, but as usual the tag location will be underlined. This option is particularly useful for exploring cases where a section of sequence has many overlapping tags. An alternative to using this dialogue is using the Control-Q key, which toggles the display of all tags.
"Set output list" pops up a dialogue asking for a list name to be used when outputting reading names. Once an output list has been specified, pressing the middle button on a reading name will add the name to the end of list. Note that selecting the same name more than once will add the name to the list more than once. The list is never cleared by the editor. This allows multiple editors to append to the same list. If required, use the list menu to clear the list.
Replacing bases or inserting new bases in the editor can assign new confidence values to those bases. The default settings set these confidence values to 100 which has the effect of forcing the consensus to be that base. The "Set Default Confidences" dialogue allows these default values to be changed. The allowable range of confidence values for a base is from 0 to 100 inclusive. The dialogue also allows selection of confidence -1. This tells the editor to not change the confidence value. When replacing a base this keeps the same confidence value of the base that is being replaced. When inserting a base this uses the average of the confidence value of the two surrounding bases.