How to Use EagleView

Once you've installed EagleView, it is easy to learn how to use it. Simply clicking open in File menu or using the shortcut "Ctl-O" to load an ACE assembly file, EagleView will display the genome assembly shortly. Before you do more clicks, it may worth spending a few minutes getting familar with different information displayed on EagleView from the following figure.

a - navigation button to previous contig
b - navigation button to previous region of the current contig
c - navigation button to next region of the current contig
d - navigation button to next contig
e - the location entry for navigation
f - information (name and number of reads) of the current contig
g - read id window showing id of the mouse pointed sequence read
h - base or genome information window display information related to mouse pointed base or region.
i - indictor of read strand (=> for forward, <= for reverse)
j - read position of the mouse pointed base
k - quality score of the mouse pointed base
l - 454 flow signal associated with the mouse pointed base
m - 454 read positions of bases called by the signal l
n - 454 no-call signal(s) immediate before the signal l
o - 454 called signal l and the number of bases it called
p - 454 no-call signal(s) immediate after the signal l
q - window scrolling bars
r - genome positions: the first one padded position (counting gaps/pads) and the second is unpadded position
s - the cursor pointing to the location in e
t - overlapping view of mapped genome features (a mutilple-line map displayed when selecting non-overlapping view)
u - Illumina/Solexa flow signal associated with the base 'A'
v - Illumina/Solexa flow signal associated with the base 'C'
w - Illumina/Solexa flow signal associated with the base 'G'
x - Illumina/Solexa flow signal associated with the base 'T'
y - the reference/concensus sequence
z - the read assembly region

Functions and Customization

EagleView is a menu-driven program with a navigation system. You can easily customize EagleView and change your preferences from its program menus. You can also use the menus and navigation system to learn all the following functions of EagleView:

  1. switch back and forth overlapping and non-overlapping view of genomic features
  2. fast naviagtion by both padded and unpadded genomice positions
  3. enable/disable genomic feature navigation by EagleView feature map file
  4. customize view window size and/or overlapping window size
  5. change background and foreground colors
  6. search a read in assembly with its ID
  7. random jump to any contig
  8. switch on/off simple view
  9. zoom in and zoom out
  10. show or hide toolbar
  11. change font type

Assembly Navigation

Standard Navigation

The assembly navigation is primarily through the four navigation buttons at the top left corner just below the menu bar. The first button (<<) and last button (>>) are for jumping to the begining and end of the contig, respectively. The second (<) and third buttons (>) are to move the view window to the upstream region and downstream region, respectively.

Navigation by unpadded/padded genomic positions

Location navigation is by entering a genomic position at the textbox at the immediate right side of the navigation four buttons. The genomic position can be either unpadded or padded genomic positions. The default position type is the unpadded position. To use the padded position, go to EagleView configure menu, and click unpadded position. To change back to use padded position, repeat the operation. You can also use the short-cut “Ctl-2” to switch quickly between padded and unpadded positions.

Navigation by genomic features

Navigation by genomic features is through the same four navigation buttons. To enable feature navigation, a customable EagleView map file containing feature location map must exist. The features can be annotated genomic features or user defined features. To switch from normal navigation to feature navigation, go to EagleView configure menu and then click feature navigation. EagleView will switch back to normal navigation mode when repeating the same operation once. In feature navigation mode, the first button (<<) and last button (>>) are for jumping to the previous and next feature positions, respectively. The second (<) and third buttons (>) are to move the view window to the beginning position of the first and last features, respectively. The short-cut “Ctl-3” can be used to enable/disable feature navigation quickly.

Navigation by contig names

The selection box next to location textbox lists all available contigs of loaded assembly file. Each value in the selection box contains contig name and number of reads in the contig. User can move view to any contig by selecting it.

Navigation by read ids

The function of Navigation by read id enable user to find location of a particular read. To find assembly location of a read, input or paste read id into read id textbox just below the navigation buttons, and click the 'Enter' key. EagleView will try to map location of the read by searching all contigs. If found, it move view to location of the read; otherwise it report no read found.

Shortcuts

EagleView also provides some convenient shortcuts for making it easy-to-use. The list of shortcuts is given at the following:

You are ready to use EagleView once you are familar with all functions and shortcuts. One more thing, EagleView aslo allows you to print out assembly view. Enjoy and Happy EagleViewing!