Ept Data - Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer User Manual

A
Appendix A Troubleshooting

EPT data

Observation
There are pull-up or pull-down
peaks in the data
(continued)
There are error messages
about spectral issues
These error messages are seen
more often in fragment analysis
data than sequence analysis
data.
There is a short read length
and uneven peak spacing in
sequence data
Fragment analysis peaks are
sized differently than previously
observed

EPT data

Observation
There is a fluctuating or
unstable electrophoresis
current, or Current check
failed is displayed
180
Possible cause
The incorrect dye set was
selected in the Plate setup.
Note: This is applicable to both
sequence analysis and
fragment analysis.
A high-quality sample has not
been run with the dye set.
The incorrect dye set was
selected in the Plate setup.
Aging of the polymer in the
cartridge, which can cause
small (≤0.5 bp) changes in
fragment size.
Possible cause
There is a bubble in the
polymer system.
The cartridge is damaged.
SeqStudio
Recommended action
Correct the dye set and repeat the injection.
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
required" on page 193.
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.
• 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.
Recommended action
Flush the capillary array.
1. Touch Settings4Cartridge4Cartridge
maintenance.
2. Touch Refresh PDS.
3. Touch to close the screen when the
function ends.
Replace the cartridge if the problem persists.
Inspect the cartridge for damage and replace
the cartridge.
Genetic Analyzer Instrument and Software User Guide
™