Thermo Scientific appliedbiosystems SeqStudio Flex Series - Page 292

Setting Description
Basecall assignment 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
End base
•
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.
Chapter 11 Manage library resources on the instrument
Analysis settings library
11
292
SeqStudio
™
Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide