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Chapter 3 Genotyping General Procedure
ChimerMarker comes preloaded with many common size standards including GeneScan 500 and LIZ600. A
custom Size Standard can be created by selecting the Size Template Editor icon next to the Size Standard field. See
Chapter 5 Fragment Sizing Standards.
Size Template Editor: This allows the user to check sample files against a selected size standard,
modify and save the size standard for future use, or create a new size standard.
Standard Color
Select the dye color which contains the internal lane standard.
Analysis Type
The Analysis Type option is inactivated in ChimerMarker.
Run Wizard Data Process
Procedure
5.
6.
The Data Process window of Run Wizard appears.
Select the appropriate analysis settings in the Data Process
window and click Next to continue.
Icons and Functions
Raw Data Analysis
Auto Range (frame)
The range in camera frames will automatically find the processable data range. If
Auto Range is not selected, manually enter the start and end frame numbers of the
data set for analysis.
NOTE: If automatic size call fails due to high saturation, de-select Auto Range and
manually input the required data range.
Intensity Coefficients: Allows for manual correction of excessive bleedthrough peaks; best used for experiments with one-color analysis. Allows for
manual correction of low RFU by using an number greater than 1 to increase the RFU
Smooth
Smoothes the baseline by eliminating smaller noise peaks.
Enhanced Smooth
This feature is used only in cases where the data is extremely difficult to analyze and cannot be corrected
with the Smooth function.
Peak Saturation
The software will analyze saturated data points by creating a synthetic estimate of the peak shape based on
the curves prior to saturation. The results will be less accurate than that of non-saturated peaks.
Baseline Subtraction
This function removes the baseline completely so that the Y-axis will be raised above the noise level. It uses
20% of lowest intensities (to the right of the beginning of the range) and looks at the trace in 500-600 frame
sections
Enhanced Baseline Subtraction
This feature is used only in cases where the data has excessive baseline in one or more of the dyes, or has an
interfering slope from the ion front in the smaller marker ranges. The function uses the second derivative of
the absolute value for every 30 data points and looks at the trace in 300 frame sections
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May 2013