Ladders

Ladders are the collection of settings that are used to identify ladder peaks in a well and then map the signal from the time domain to the base size domain, providing the base size of a given peak. MicroSPAT currently provides a cubic spline interpolation method that generates a sizing quality metric which is essentially the weighted sum of squared residuals of the spline approximation.

Register New Ladder

Navigate to the Ladders tab on the left side. Populate the fields to the right with relevant information. At a minimum provide a unique label, a comma separated list of the base sizes of expected peaks, and the color of the dye used for this ladder. Scanning Parameters may be manipulated to affect how peaks are initially identified during ladder determination.

Settings

Parameter	Description
Label	The unique label to identify ladder settings
Bases (Comma Separated)	Comma separated list of expected base sizes for peaks in ladder
SQ Flagging Limit	Maximum Sizing Quality value allowed before flagging a well as having a ladder sizing issue
SQ Unusable Limit	Maximum Sizing Quality value allowed before completely ignoring a well for downstream processing
Base Size Precision	Precision after decimal point for interpolating base size. In general does not need to exceed 2
Index Overlap	Minimum number of data points between peaks, used for culling out false peaks and stutter in ladder determination
Min. Run Time	Discard data points before this value, used for culling out false peaks from beginning of run
Max. Peak Height	Remove peaks found to be greater than Max. Peak Height, used for removing outlier peaks due to bleedthrough from other channels
Min. Peak Height	Remove peaks found to be less than Min. Peak Height, used for removing outlier peaks attributable to low level noise and bleedthrough from other channels
Outlier Limit	Cull peaks that are outliers by height until only a set of peaks of length Bases + Outlier Limit exists, then use iterative algorithm to determine best fit curve to interpolate base sizes
Maximum Missing Peak Count	Maximum number of peaks that may be missing before ladder interpolation fails
Remove Outliers	Remove outliers in initial pass before applying iterative algorithm (Setting to true is in general faster)
Allow Bleedthrough	True => Keep peaks even if potential bleedthrough detected, False => Remove peaks where potential bleedthrough detected (Set to false if having issues with bleedthrough peaks being detected as real peaks)
Color	The color of the channel used for the ladder