Observation
Possible cause
Recommended action
There are pull-up or pull-down
peaks in the data
(continued)
The incorrect dye set was
selected in the Plate setup.
Note:
This is applicable to both
sequence analysis and
fragment analysis.
Correct the dye set and repeat the injection.
There are error messages
about spectral issues
These error messages are seen
more often in fragment analysis
data than sequence analysis
data.
A high-quality sample has not
been run with the dye set.
If the dye set is a fragment analysis dye set
that is being used for the first time, run a
manual dye calibration.
Alternatively, if a high-quality sample is run
with an uncalibrated dye set, and the
automated spectral calibration successfully
generates an optimized matrix, manual
calibration is not absolutely required. See
“Determine if manual calibration is
There is a short read length
and uneven peak spacing in
sequence data
The incorrect dye set was
selected in the Plate setup.
Correct the dye set and repeat the injection.
Select from the following:
• E_BigDye
™
Terminator v1.1
• Z_BigDye
™
Terminator v3.1
• Z_BigDye
™
Direct
Reanalyze the data in the Sequencing Analysis
Software, using the correct mobility file.
Fragment analysis peaks are
sized differently than previously
observed
Aging of the polymer in the
cartridge, 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
• Manually adjust the fragment bin
positions to account for the size change.
EPT data
Observation
Possible cause
Recommended action
There is a fluctuating or
unstable electrophoresis
current, or Current check
failed is displayed
There is a bubble in the
polymer system.
Flush the capillary array.
1. Touch Settings
4
Cartridge
4
Cartridge
maintenance.
2. Touch Refresh PDS.
3. Touch to close the screen when the
function ends.
Replace the cartridge if the problem persists.
The cartridge is damaged.
Inspect the cartridge for damage and replace
the cartridge.
Appendix A
Troubleshooting
EPT data
A
180
SeqStudio
™
Genetic Analyzer Instrument and Software User Guide
