Loading Annotation

Annotation can only be loaded after at least one map has been loaded. If you need to load a map, you can follow the instructions on how to Load a Map.

How to Load Annotation

1. To load annotation select, "Annotation -> Load Annotation..." from the menu or use the keyboard shortcut "Ctrl + A".

   

2. When the "Load Annotation" dialog box opens, select the type of annotation you wish to load from the drop down menu pictured below.

   

3. After you have chosen which type of annotation you want to load, you need to choose which map(s) you would like to load annotation for. By default VCMap will load the annotation for each map you currently have loaded (even if the map is hidden). If you are going to load the annotation for all of the maps, continue to step 5.
   Note: Not all types of annotation will be available for every map. The maps listed are the maps for which the current type of annotation can be loaded for.
4. The loaded maps will initially all be selected. To load annotation for only one map, click on the map. The chosen map name will be highlighted. To load annotation for multiple maps, the Ctrl key needs to be pressed. While holding the Ctrl key, use the mouse to toggle (between selected and not selected) which maps annotation will be loaded for. The maps will toggle by simply clicking on the name while the Ctrl key is pressed. A map is chosen when its name is highlighted.
   Note: Not all types of annotation will be available for every map. The maps listed are the maps for which the current type of annotation can be loaded for.
   
   
   
5. If you are not loading QTL data then click the "Load" button to load the annotation you have chosen. If you are loading QTL data, continue on to step 6.
   Note: Once the dialog box closes, it will take a few moments fot the annotation to load.
6. When loading QTL data, you have the option to apply ontology filters to the data. The drop down menu lists all of the ontology filters. Terms that are in black with a number next to them are filters that can be loaded for the maps selected in steps 3 and 4 above (the numbers indicate how many pieces of annotation are under the filter). Terms in gray are filters that are available on a different chromosome of the selected map(s). (Available filters will always be listed at the top of the list. Unavailable filters will be at the bottom)

   

7. Chosen filters will be listed in a tree structure under the drop down menu. The drop down menu will change update to reflect which filters have been selected. It will contain subcategories of the previously chosen filters.
   Note: There will be a varying amount of subcategories depending on which filters are chosen.

   

Additional QTL Information:

• Filters can be removed from the selection by using the tree. Clicking on the filter you wish to go back to will remove all filters that are subcategories of it.
• You can load at any time. Clicking "Load" will load all data that is a subcategory of the last chosen filter. You do not need to choose subcategories until there are no more to choose.
• Loading all available QTL data is done when "All Data" is the only item in the tree.
• After QTL has been loaded and is visible on the map, you can check which filters have been loaded on a particular map by clicking on the "QTL" label above the column.

  Note: Even if no QTL exists on a map but was chosen to be loaded for it, it will be in the list. In the above picture, a Bos Tauraus map is also loaded. The "production" filter was chosen to be loaded for both maps. This filter only exists on Bos Taurus but since it was chosen to be loaded for the Homo Sapiens map also, it appears in the listing.

See Also

• Load a Map
• Download Annotation Information