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Chapter 3 Genotyping General Procedure
Pullup Correction
Ax=B
A being the major coefficient
Input matrix or use single dye adjustment up to 0.20 for small corrections
When Manual Pullup correction is chosen, a .txt or .mtx matrix file can be uploaded and used to deconvolute
dye colors.
NOTE: De-select automatic Pullup Correction in the Run Wizard Data Process box if a manual matrix correction
has been applied.
Saturated Peak Correction
ABI instrument saturated peaks are typically >8000 RFU
The top of a saturated peak looks split
A small pullup peak may be present under the saturated peak
ChimerMarker takes the small pullup peak and adds it to the split in the saturated peak
Spike Removal
Caused by overheating of camera chip, voltage spike, etc
Spikes usually only 1-2 frames wide; peaks usually 5-10 frames wide
Create a first derivative trace of the raw data
Spikes are the 1st DT outliers (3-5 sigma)
Second Derivative Trace
(A1-A2)-(A2-A3) = A1+A3-2(A2)
Use when you have a fat base to your peaks (ex. Dye blob under peak, etc)
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May 2013