GeneMapper 3.7 Tom Devitt 12/6/05. Password: dnapass User Name: gm (should be automatic)

GeneMapper 3.7

Tom Devitt

12/6/05

Password: dnapass

User Name: gm (should be automatic)

File, add samples to project

Navigate to the folder containing your samples

select

‘Add to List’

Then click ‘Add & Analyze’

Name your project (e.g. EXP40_ENS2)

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

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.

Next, click on ‘Panel Manager’

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

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

Click once on the kit you just made

Then File -> New Panel (name panel by locus)

Click once on the panel you just made

Then File -> New Marker

Name marker by locus Specify color of your

labeled primer

specify min and max size of your marker (50-450 bp)

Specify marker repeat # (e.g., 4 for tetranucleotide)

Go back to kit, click once to highlight

Then go to ‘Bins’ -> ‘New Bin Set’

Name by locus

Then close Panel Manager by clicking OK at the bottom of screen

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)

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

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

Then go to Bins, select Auto Bin

Select Rounded basepair and Auto Bin and click OK

Click OK to get out of Panel manager

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

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

Reanalyze

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)