Transcript Genemapper for Dummies - Museum of Vertebrate Zoology

GeneMapper 3.7
Tom Devitt
12/6/05
User Name: gm (should be automatic)
Password: dnapass
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 marker
repeat # (e.g., 4 for
tetranucleotide)
specify min and max size of your marker
(50-450 bp)
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)