genemapper 3.7 tom devitt 12/6/05. password: dnapass user name: gm (should be automatic)
TRANSCRIPT
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GeneMapper 3.7
Tom Devitt
12/6/05
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Password: dnapass
User Name: gm (should be automatic)
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File, add samples to project
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Navigate to the folder containing your samples
select
‘Add to List’
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Then click ‘Add & Analyze’
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Name your project (e.g. EXP40_ENS2)
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To see if your run worked, select all samples (ctrl+A), and click ‘Display Plots’:
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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.
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Next, click on ‘Panel Manager’
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New window will appear; in upper left corner, click on panel manager
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Go to File -> new kit (name kit by locus); choose kit type from drop down menu (e.g. microsatellite)
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Click once on the kit you just made
Then File -> New Panel (name panel by locus)
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Click once on the panel you just made
Then File -> New Marker
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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)
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Go back to kit, click once to highlight
Then go to ‘Bins’ -> ‘New Bin Set’
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Name by locus
Then close Panel Manager by clicking OK at the bottom of screen
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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)
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Go back to panel manager, select your marker (click once) then go to Bins -> Add Reference Data
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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
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Then go to Bins, select Auto Bin
Select Rounded basepair and Auto Bin and click OK
Click OK to get out of Panel manager
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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
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Under the General tab, name the Analysis Method by your locus; under the Allele tab, choose your Bin Set; then click ok
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Reanalyze
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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)