Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer User Manual page 145

Setting
Baseline Window
Minimum Peak Half Width
Peak Window Size
Polynomial Degree
Slope Thresholds Peak
Start and End
SeqStudio Genetic Analyzer Instrument and Software User Guide
™
Specify a window to adjust the baseline signals of all detected dye colors to the same
level for an improved comparison of relative signal intensity. Note the following:
• A small baseline window relative to the width of a cluster, or grouping of peaks
spatially close to each other, can result in shorter peak heights.
• Larger baseline windows relative to the peaks being detected can create an
elevated baseline, resulting in peaks that are elevated or not resolved to the
baseline.
Specify the minimum full peak width at half maximum Peak Height required for peak
detection. The range is 2 to 99 data points.
Enter a window width in data points for peak detection sensitivity. If more than one
peak apex is within the window, all are labeled as a single peak. Note the following:
• The maximum value is the number of data points between peaks.
• The Peak Window Size setting is limited to odd numbers.
To increase peak detection sensitivity: Increase polynomial degree, decrease peak
window size. To decrease peak detection sensitivity: Decrease polynomial degree,
increase peak window size.
Polynomial Degree cannot be greater than Peak Window Size.
Adjust to affect the sensitivity of peak detection. You can adjust this parameter to detect
a single base pair difference while minimizing the detection of shoulder effects and/or
noise.
The peak detector calculates the first derivative of a polynomial curve fitted to the data
within a window that is centered on each data point in the analysis range.
Using curves with larger polynomial degree values allows the curve to more closely
approximate the signal and, therefore, captures more of the peak structure in the
electropherogram.
• Peak Start—The peak starts when the first derivative (slope of the tangent) in the
beginning of the peak signal before the inflection point becomes equal to or
exceeds the Peak Start value. This threshold is set to 0 by default, which means
that the peak will normally start at the leftmost point where the slope of the
tangent is closest to 0° (horizontal line). A value other than 0 moves the peak start
point toward its center. The value entered must be non-negative.
• Peak End—The peak ends when the first derivative (slope of the tangent) in the
end of the peak signal after the inflection point becomes equal to or exceeds the
Peak End value. This value is set to 0 by default, which means that the peak will
normally end at the rightmost point where the slope of the tangent is closest to 0°
(horizontal line). A value other than 0 moves the peak end point toward its center.
The value entered in this field must be non-positive.
Using curves with larger polynomial degree values allows the curve to more closely
approximate the signal and, therefore, captures more of the peak structure in the
electropherogram.
Chapter 10 Manage the software (instrument)
Manage run settings (instrument)
Description
10
145