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Appendix A Troubleshooting
A
QC error and alert troubleshooting
QC errors—Sequencing
See also "Sample QC and quality alerts"
QC error
Basecalling failed due to poor
quality data.
or
Basecalling failed, possibly due
to insufficient data collected, or
incorrect analysis settings.
or
The trace score is lower than 30.
The trace score is lower than 15.
QC errors—Fragment analysis
See also "Sample QC and quality alerts"
QC error
Sizing quality value is low due to poor size
standard peak quality. Peak height uniformity
is low or the fitting quality in sizing is poor.
Sizecaller found broad peak(s) in the size
standard peak(s).
Sizing quality value is in the intermediate
range; check size standard data quality.
Sizing quality value is in the failing range;
check size standard data quality.
490
on page
172.
Description
Poor quality data is present.
The sequence in the sample is too
short to basecall.
The incorrect dye set definition is
specified in the plate file.
on page
172.
Description
Low resolution or poor-quality
data is present.
• Pass ≥0.75
• Intermediate 0.25 to <0.75
• Fail <0.25
SeqStudio
™
Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide
Action
• Ensure that no consumables
have expired. See "Check
consumables status"
page
66.
• Re-inject the sample.
• If the problem persists, prepare
fresh sample.
• Check the sample quality.
• Check the template quality and
quantity.
• Troubleshoot upstream PCR and
sequencing steps.
Use a longer amplicon.
Select the dye set that matches the
chemistry that you are running.
™
If you use the BigDye
Direct
Cycle Sequencing Kit, use the
Z_BigDye Direct dye set, not the
Z_BigDye Terminator v3.1 dye set.
For more information, see "Using
BigDye
™
Direct Cycle Sequencing Kit
chemistry"
on page
312.
Action
• Ensure that no
consumables have
expired. See "Check
consumables status"
page
66.
• Re-inject the sample.
• If the problem persists,
check the sample quality.
on
on
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Table of Contents
Troubleshooting
