Data Loading

First, we’ll load the genetic maps. The wizard is accessible through the “File” menu and “Genetic data loading” sub menu. Choose “New project” and name it “data”.

Create new project

The next step is the files choosing; browse your files and select all files inside the “tutorial/Genetic Files” folder. (hold the “shift” or “control” button to select all files, or press the combined keys “Control” and “a” (replace “control” by the “apple” key on mac OS))

Genetic maps loaded

The next step shows a summary on all loaded files.

Once the wizard is finished, the new maps will be displayed in the explorer on the left side, inside the chosen project. You can delete a single map, click right on the map Laurence and then click on supress button.

Maps explorer on the left

Chromosomes display

For displaying a whole map, click on the map in the explorer, move the mouse in the drawing panel and release the mouse button. The whole map should appear with all chromosomes and linkage groups. You can drag an drop a chromosome or linkage group the same way. Drag the chromosomes ‘1’ from ‘Cardinal_2001’, ‘Groh_1998’ and ‘Mechin_2001_inv1’ maps to see the dynamic comparison. You see now the common markers linked with blue and red lines; red lines show the inverted markers. Now drag the ‘Mechin_2001_inv1’ from the right side to the left side of ‘Groh’_1998’ by moving it (holding the mouse left button). We see lots of inversion; right click on the ‘Mechin_2001_inv1’ and select “Reverse linkage group”; the whole linkage group is now in the right order. To remove an element from the display panel, you have 2 ways : * use the middle click of the mouse on the element to remove * right click on the element, then select “remove from view” in the contextual menu

Chromosome display

Individual zoom

Drag several chromosomes into the display panel; now, put the mouse inside a chromosome, and use the mouse wheel; you will zoom inside the chromosome, keeping other chromosome un-zoomed. (You can also right click on the chromosome, and choose “Zoom in/out”. To keep an idea of your position in the chromosome, a mini-chromosome is displayed below, with a scroller indication your viewing window. (Try this functionality a bit later on chromosomes with more markers on them.)

Individual zoom

Cascading zoom

Clear the drawing panel and drag the chromosome 8 from ‘Chardon_2005a’. Clicking on it will launch the cascading view; a scroller appears and can be move/resized with your mouse for exploring the chromosome with more details.

Fig6 here

You can click on the zoomed chromosome for more details.

Cascading zoom

The zoom allows to display more information on the markers; (some markers are hidden by default when there are too many; this option can be changed in the “Expert” tab, below the maps explorer).

Next step