This tab has been redesigned and expanded in IGB 6.6. This tab contains options addressing the color/appearance of non-track elements in the image, as well as some other miscellaneous options.
Coordinates
These are options for changing number appearance. FULL shows the number with no thousands separators and the unit 'kb'. COMMA shows the numbers with commas at every 10^3 (U.S. style) and with no unit designations. This is the default. ABBREV will show the numbers as abbreviated as is reasonable, with unit designations. For example, when zoomed out, numbers appear as 10M, 20M etc. Changes made here to Number Format take effect immediately.
You can change the foreground and background colors from the Preferences > Tracks tab or the Annotation tab.
Residue Colors
IGB highlights each residue in a different color when zoomed in. By default, IGB uses cool colors for A and T residues and warmer colors for G and C residues. Other refers to residues that are either 'N', 'X' or '-' (missing) and can be set to a bright color if you are looking for deletions in short read sequences; otherwise you may wish to leave it as the neutral gray.
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If you do NOT wish for individual residues to be highlighted, set the colors to white or a light grey. Another great color scheme, if you are looking for CpG islands, is to set A and T to a neutral white or grey, make C a bright red and then G a moderate blue - this makes it easy for the eye to pick out the CG combination when skimming across genomic DNA. |
ORF (Open Reading Frames) Analyzer
These preferences affect colors used to indicate stop codons, the ORFs and the background of the ORF tracks that are shown in the Sliced View tab.
Edge Match
The Edge Match feature can be changed to a color more suited for your background color. The default shows white, with the navy blue annotations and the gray background. If you chose a lighter background, we recommend a darker color here. If you do NOT watch the edge match feature to show, uncheck the Show Edge Matching box.
Codon Display
The Codon Display is activated when the sequence of a gene model is loaded and the user zooms in close enough to see the sequence. The codon translation appears within the gene model. User can set the amino acids to appear in one letter format (default), three letter format or be hidden. The colors is based on the chosen foreground color for the track.
Track Resize Behavior
Track Resize Behavior is how IGB adjusts other tracks when a specific track height is changed. Adjust All Tracks means that as a single track is increased in height, all other tracks are reduced by a commensurate amount. Adjust Adjacent Tracks (default) means that all added or subtracted height is removed/added to the bordering track, leaving the rest of the display unaffected.
Miscellaneous Options
IGB has included an option for the Prototype - View Mode, which will automatically change the default view to a depth graph view as you zoom out past a threshold. Details can be found Prototype - View Mode.
Confirmations
IGB warns you when you are about to exit the program and before you delete a file or files. Each of these warnings has the option to not be shown again. To turn off these warnings or reset your previous choice, check (or uncheck) Ask before exiting and/or Confirm before deletethese options.
Reset all preferences to defaults
Click Reset preferences to defaults to reset all the preferences to the IGB defaults. This is sometimes useful if you need to troubleshoot IGB.
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