QC errors—Sequencing
See also “Sample QC and quality alerts” on page 172.
QC error Description Action
Basecalling failed due to poor
quality data.
or
Basecalling failed, possibly due
to insucient data collected, or
incorrect analysis settings.
or
The trace score is lower than 30.
The trace score is lower than 15.
Poor quality data is present.
•
Ensure that no consumables
have expired. See “Check
consumables status” on
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.
The sequence in the sample is too
shor
t to basecall.
Use a longer amplicon.
The incorrect dye set definition is
specified in the plat
e file.
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.
QC errors—Fragment analysis
See also “Sample QC and quality alerts” on page 172.
QC error Description Action
Sizing quality value is low due to poor size
standar
d peak quality. Peak height uniformity
is low or the fitting quality in sizing is poor.
Low resolution or poor-quality
data is present.
•
Ensure that no
consumables have
expired. See “Check
consumables status” on
page 66.
•
Re-inject the sample.
•
If the problem persists,
check the sample quality.
Sizecaller found broad peak(s) in the size
standard peak(s).
Sizing quality value is in the intermediate
range; check size standard data quality.
•
Pass ≥0.75
•
Intermediate 0.25 to <0.75
•
Fail <0.25
Sizing quality value is in the failing range;
check size standard data quality.
Appendix A Troubleshooting
QC error and alert troubleshooting
A
490
SeqStudio
™
Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide
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