Section 2 New Features: All AmpF l STR Kits
Section 2 New Features: All AmpFlSTR Kits
This section covers:
New Features Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Export Combined Table Format . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Changes to the Electropherogram Displays . . . . . . . . . . . . . . . . . . 22
New Features Summary
Table 1 below provides a brief summary of the new features included
in GeneMapper ID Software v3.2. For more detailed information, see the pages referenced in the table.
Table 1 New features summary
Feature Description
Export Combined Table format
• When exporting from the Samples view, you can now export samples that do not pass sizing along with samples that pass sizing. This feature combines columns from the sample table and the genotype table and exports them as a single table.
• You now have two display options when exporting samples:
– One line per marker
– One line per sample (This is similar to the Make Allele table in the Genotyper ® Software.)
Changes to the electropherogram displays
• The software now provides the option to display labeled peak assignments for all size standards. This allows you to quickly identify peaks visually and perform a size precision test.
The labeled peak assignments are printable.
• When switching from the “align by base pair” to the “align by data point” views for the X-axis, the labels associated with the peaks are now retained in both views.
See
Page
18
37
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Export Combined Table Format
GeneMapper ID Software v3.2 can export data in the Export
Combined Table format. This new format:
• Allows you to track all samples in an electrophoresis run. That is, when exported from the Samples view, samples that do not pass sizing are exported along with samples that pass sizing.
• Provides two display options: one line per marker and one line per sample
Size Quality
Status in the
Samples View
As shown in Figure 1
below, the size quality status is displayed in the
SQ column of the Samples view:
• Samples that do not pass sizing are flagged with a red circle.
• Samples that pass sizing are flagged with a green square.
When you create an Export Combined Table, both the passing and
low-quality samples are exported together, as shown in Figure 2 on page 19 and
Figure 3 on page 20
. The procedure for creating an
Export Combined Table is on
page 20 .
These samples do not pass sizing.
These samples pass sizing.
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Figure 1 Size quality status
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Export Combined Table Format
Two Export
Display Options
Two display options are available to export samples that do not pass sizing with samples that pass sizing:
• One line per marker
This option displays information for each marker on a separate line for a given sample. In
Figure 2 below for example, lines 2
through 15 display the information for each marker in sample file A1012531.fsa.
Figure 2 One line per marker
Installation Procedures and New Features for GeneMapper ® ID Software v3.2
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GeneMapper ® ID Software
• One line per sample
This option displays the information for each sample on just one
line. In Figure 3
below for example, line 2 displays information for Sample Name 12531. The subsequent lines display information for different samples.
Figure 3 One line per sample
Creating an
Export Combined
Table
To create an Export Combined Table:
1.
After analyzing your samples, go to the toolbar and select
File > Export Combined Table to open the Export
Combined Table window.
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Export Combined Table Format
To create an Export Combined Table:
2.
From the Look in drop-down list, select an appropriate destination folder for the Export Combined Table.
3.
From the Export File As drop-down list, select a file type.
4.
From the Merge panel, select the format style:
• One line per marker, or
• One line per sample
Note: format.
See page 19 and
page 20 for an example of each
5.
If you selected One line per marker in step 4
, select/deselect the Include all marker information checkbox, as necessary.
As shown in the pop-up text below, if you select this option, marker information for samples with no sizing data will be included in the Export Combined Table.
6.
Type in a File name.
7.
From the Files of type drop-down list, select the appropriate file type/extension.
8.
Click Export Combined Table.
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Changes to the Electropherogram Displays
In GeneMapper ID Software v3.2, two changes have been made to the electropherogram displays:
• Labeled peak assignments can be displayed for all size standards
• Labels are retained in both the “align by base pair” and “align by data point” views for the X-axis
Labeled Peak
Assignments for
All Size
Standards
GeneMapper ID Software v3.2 now provides the option to display labeled peak assignments for all size standards in the electropherograms. (That is, all defined size standard peaks are labeled in the electropherogram per the size standard definitions).
This allows you to quickly identify peaks visually and perform a size precision test.
To display peak assignments for all size standards:
1.
In the Samples view, highlight all sample files in the project.
2.
Click the Display Plots icon.
3.
From the Plot Setting drop-down list, select AmpFLSTR
Genotyping.
4.
Hide all dyes except the size standard dye (that is, red for
ROX ™ dye or orange for LIZ ® dye).
5.
Select View > Show Size Standard Label.
6.
Verify that all values for the 250-bp fragment peaks are within
± 0.5 bp.
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Changes to the Electropherogram Displays
To display peak assignments for all size standards: (continued)
7.
If desired, select File > Print to print the electropherogram plots. The examples below show both labeled and unlabeled peak assignments.
Labeled peak assignments
Unlabeled peak assignments
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Labels Retained in Base Pair and
Data Point Views
The X-axis can be displayed in either base pairs or data points. In
GeneMapper ID Software v3.1, when switching from the “align by base pair” to the “align by data point” views for the X-axis, the labels associated with the peaks were not retained in both views. In
GeneMapper ID Software v3.2, the labels are automatically retained in both views, as shown below.
Figure 4 Align by base pair
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Figure 5 Align by data point
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