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