Option
If checked, the software creates…
Processed Data Determines scaling of the processed traces. This parameter does not affect the
accuracy of the basecalling.
• True Profile—The processed traces are scaled uniformly so that the average height
of peaks in the region of strongest signal is about equal to a fixed value. The profile
of the processed traces will be very similar to that of the raw traces.
• Flat Profile—The processed traces are scaled semi-locally so that the average
height of peaks in any region is about equal to a fixed value. The profile of the
processed traces will be flat on an intermediate scale (> about 40 bases).
Ending base Last base on which to perform basecalling:
• At PCR Stop
• After X number of Bases
• After X number of Ns in X number of Bases
• After X number of Ns
Note: If you have PCR products with sequences that end while data is still being
collected, select the At PCR Stop check box.
Quality Threshold
• Do not assign N's to Basecalls —When using the KB
™
basecaller, use this option to
assign a base to every position, as well as the QV.
• Assign N's to Basecalls with QV<15 — When using the KB
™
basecaller, use this
option to assign Ns to bases with QVs less than the set point. The QV is still
displayed.
Mixed Bases Note: This function is active with the KB
™
Basecaller only.
When enabled, determines the secondary peak height ratio where the secondary peak is
considered a potential mixed base. Reaching the threshold is a necessary but not
sufficient condition for the basecalling algorithm to call a mixed base.
Clear range methods
• Use clear range minimum and maximum—Specifies the first and last base in the
range to consider, or trims the specified number of bases from the 3¢ end.
• Use quality values—Sets a window with a specified number of allowed low-quality
bases by removing bases until there are < X number of bases per Z number of
bases with QV < Y.
• Use identification of N cells—Sets a window with a specified number of allowed
ambiguous base calls (Ns) by removing bases until there are < X number of Ns per
Y number of bases.
Chapter 7 Create and manage instrument protocols, run modules, and analysis protocols
Create an analysis protocol
7
90
3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide
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