Observation Possible cause Recommended action
Extra peaks are present in the
sequencing traces
(continued)
The PCR amplification primers
do not have specificity and
are sequencing two dierent
regions of the genome. The
analyzed trace shows extra
peaks throughout the entire
length of the trace.
Redesign the primers or increase the
amplification temperature.
You accidentally contaminated
the DNA and are sequencing
two templates at the same
time. The analyzed trace shows
extra peaks throughout the
entire length of the trace.
Repeat the amplification and sequencing
reactions with uncontaminated DNA.
There were impure or
contaminated primers.
Primer stocks may have inadvertently had
other primer solution introduced. For best
results, use HPLC to purify the primers.
There was a contaminated
sample well.
Use a new sample plate and buer/wash
septa whenever possible.
To avoid getting sample into adjacent wells,
centrifuge the plates before you remove the
adhesive seal.
Fragment analysis applications
Observation Possible cause Recommended action
Fragment analysis peaks are
sized dierently than previously
observed
Aging of the polymer, which
can cause small (≤0.5 bp)
changes in fragment size.
•
Use a reference marker (for example, an
allelic ladder) for auto bin adjustment.
Or
•
In secondary analysis software, manually
adjust the fragment bin positions to
account for the size change.
Settings screen troubleshooting
Observation Possible cause Recommended action
All buttons except About and
SAE ar
e inactive
SAE mode is enabled on the
instrument and you are signed
in as a local administrator.
No action. Normal occurrence.
The SAE button is not
displayed in the Instrument
Settings screen
SAE has not been enabled by a
service representative.
Contact Technical Support.
Appendix A Troubleshooting
Settings screen troubleshooting
A
SeqStudio
™
Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide
519
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