Resize:  The Resize tool allows you to change the 'Width' and 'Start Position' settings using the mouse.  Moving from side to side will change the width. Moving the mouse up and down scroll to new starting positions in the file.  Since the display is laid out in the same way as a scrolling text file 'up' is the start of the file and 'down' is the end of the file.

Move: The Move tool is simply an easy way to use the scroll bars.  It will scroll the screen up and down or side to side.  The Horizontal Scrollbar will appear anytime the display is wider than the screen.

Select: Use this tool when you want to know the exact position or sequence at a given location.  The cursor is a cross-hair that you can point at a specific pixel.  Clicking a pixel will dump the information to the text box at the bottom of the screen.  The Select tool has a yellow pixel directly underneath the cursor as an aid.  If you are having trouble being exact, try increasing the "Zoom" variable.  

As a convenience, you may also use the keyboard to change the start position and width.  Click on the main canvas to set the keyboard focus then use the following keys:

Up Arrow = scroll data up 10 lines

Down Arrow = scroll data down 10 lines

Left Arrow = Decrease Display Width

Right Arrow = Increase Display Width

 Clicking on other boxes will set the keyboard focus to that box.  For example, if you click on the "Zoom" box, the up or down arrow key will modify the value of Zoom.

 

 

There are a number of different Graph Modes in Skittle.  Each graph is a visual representation of the raw data in the FASTA file.  Each mode has its own uses and highlights different features of the data. A detailed discussion of each mode is covered in the technical paper.  You can toggle the Graph Mode on or off and display several side by side.

Nucleotide Display - the simplest display where nucleotides equal colors.

 

Repeat Overview - Color indicates the best alignment from 1-250.  The brighter a color is the better the match.  Areas that don't align well appear as darker colors.  (Minimum Scale = 4)

 

Repeat Map - repeat detection. Repeats of the same sequence appear as white pixels.

 

Sequence Highlighter - This highlights nucleotides based on whether they match a user search string.  Use the Sequence Highlighter Settings tab in the Information Display to set the Highlight Sequence.

 

 

Open File - Open a new file in the current window.

 

New Window - Create a new window.  Multiple windows are useful when comparing similar files.

 

Add Annotation - Open a dialog for adding a new annotation entryat your current location.  The Start and End values are automatically set to the size of the window currently displayed, but you may change these to any value.  The output format is the GTF genome annotation.  You can also Load GTF annotation through File > Open GTF File.  If you are adding to an annotation you are currently viewing, the display will be updated with your new notes.   The new annotation is added to a Skittle notes file specifically created for user created notes.  The file name of the annotation file is: "<filename>-skittle_notes.gtf".  This file will be created in the same directory as the open data file.  One notes file is created for each for each individual data file.

 

 

Width - The number of base pairs one row on the display represents.

 

Scale - The number of base pairs one pixel represents.  Changing scale also changes Width so that the number of visual pixels remains the same.

 

Zoom - This adjusts the physical size of each Skittle "pixel" on the display.  As a data visualization, Skittle "pixels" do not have a 1:1 correlation with the pixels of a computer monitor.  Note that SCALE is the best variable to adjust in order to "zoom out" to see an entire chromosome.

 

Start - The index of the first nucleotide displayed on the screen.  This variable allows one to scroll through an entire chromosome.  The Move and Resive tools modify this variable as well.

 

Display Length - This is the number of base pairs that are currently visible on the screen.  The program automatically adjusts the Display Length to match the width and height of the display so this variable is for informational purposes only.  It has a minimum value of 1,000bp for the purposes of facilitating the sequence analysis tools in Skittle.

 

Sync Windows - If this is checked, then all open windows use the same set of display variables.  This is useful when comparing two similar files.  You can use Offsets to compensate for changes in sequence alignment between files.  If you have multiple, unrelated files open, uncheck "Synchronize Windows" so that browsing one file will not affect any others.

Offsets - Each window has an offset which adds allows that window to scroll independently.  The displayed position in the sequence is the Start Index plus that windows Offset.  While browsing a chromosome Offset can be easily changed with the Resize or Move tools by holding the Control Key while clicking and dragging the mouse.