1. GeneMapper 3.7
Tom Devitt
12/6/05

2. User Name: gm (should be automatic)
Password: dnapass

3. File, add samples to project

4. Navigate to the folder containing your samples
select
‘Add to List’

5. Then click ‘Add & Analyze’

6. Name your project (e.g. EXP40_ENS2)

7. To see if your run worked, select all samples (ctrl+A), and click ‘Display Plots’:

8. You will see peaks if your run worked
You will see peaks if your run worked. Play around with the buttons at the top to change the window size, colors, number of samples, etc., that are displayed.

9. Next, click on ‘Panel Manager’

10. New window will appear; in upper left corner, click on panel manager

11. Go to File -> new kit (name kit by locus); choose kit type from drop down menu (e.g. microsatellite)

12. Click once on the kit you just made
Then File -> New Panel (name panel by locus)

13. Click once on the panel you just made
Then File -> New Marker

14. Specify marker repeat # (e.g., 4 for tetranucleotide)
Name marker by locus
Specify color of your labeled primer
specify min and max size of your marker ( bp)

15. Go back to kit, click once to highlight
Then go to ‘Bins’ -> ‘New Bin Set’

16. Name by locus
Then close Panel Manager by clicking OK at the bottom of screen

17. Go back to project window, change panel name to the one you just made (ctrl+d to fill down) and REANALYZE with new panel chosen – hit green arrow button (otherwise reference data won’t show up in panel manager when you’re trying to autobin)

18. Go back to panel manager, select your marker (click once) then go to Bins -> Add Reference Data

19. A new window will appear; highlight the folder(s) containing your samples; click Add To List (they’ll move to the right hand column); click Add

20. Then go to Bins, select Auto Bin
Select Rounded basepair and Auto Bin and click OK
Click OK to get out of Panel manager

21. Go back to project window and make a new analysis method:
Click on a cell in the Analysis Method column, and select new analysis method
A new window will appear; select Microsatellite and then OK

22. Under the General tab, name the Analysis Method by your locus; under the Allele tab, choose your Bin Set; then click ok

23. Reanalyze

24. Some additional notes. . .
Check question marks in genotypes; delete them once you’ve checked them
In the genotypes plot view, can move bins around as long as you’re in ‘Binning Mode’
When editing bins in the genotype plot, save a ‘project’ AND DON’T REANALYZE OR ADD SAMPLES SUBSEQUENTLY
Can import bin sets and settings for subsequent samples for same locus (tip from RE Bingham)