Thermo Scientific appliedbiosystems SeqStudio Flex Series User Manual page 292

Chapter 11 Manage library resources on the instrument
11
Analysis settings library
Setting
Basecall assignment
End base
292
The basecaller assigns one basecall per position from IUPAC code options:
A, C, G, T, R, Y, S, W, K, M. This setting determines how to analyze a
basecall with a low quality value (QV), where N is any N is any call, per
IUPAC code.
• Do not assign Ns to basecalls (default)
• Assign Ns to basecalls with QV<X—Basecalls with a QV less than the
X threshold display N instead of the base letter
• At PCR stop (default)
• 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 checkbox.
Note: The default sequencing analysis settings are optimized for PCR
amplicon sequencing. For sequencing of plasmid templates, create analysis
settings with the following selections: for the End base setting, deselect At
PCR stop; for the Mixed base threshold setting, deselect Use Mixed base
identification.
SeqStudio ™ Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide
Description