Sample and data troubleshooting
See also “Data quality alerts“ on page 119, “Sizecalling and basecalling quality
alerts“ on page 119, and Troubleshooting Sanger sequencing data User Bulletin
(Pub. No. MAN0014435).
Observation
Possible cause
Recommended action
Offscale signal is detected is
displayed
Note:
Samples are stable on
the instrument for 16–24 hours.
Determine if samples will be
stable if a re-injection is
recommended, then plan the
re-injection accordingly.
The sample concentration is
too high.
Dilute the sample, prepare a new plate, and
start a new run.
Quantitate the sample prior to adding reagents
for capillary electrophoresis.
The injection conditions are too
strong for the sample.
Re-inject the samples with adjusted injection
conditions.
Injection time, voltage, or a combination of
these conditions can be adjusted.
There is no signal or a low
signal
Note:
Samples are stable on
the instrument for 16–24 hours.
Determine if samples will be
stable if a re-injection is
recommended, the plan the re-
injection accordingly.
The sample volume was
insufficient.
Use the recommended sample volume.
See “Sample preparation guidelines“ on
The sample concentration was
too low.
Re-inject the samples with adjusted injection
conditions.
Injection time, voltage, or a combination of
these conditions can be adjusted.
There were bubbles in the
sample wells.
Centrifuge the sample plate or tubes to remove
the bubbles before loading onto the
instrument.
If the samples have been run, centrifuge the
plate or tubes, then set up a re-injection.
The sequence reaction failed.
Review the sequence analysis protocol, the
template quality, and the template quantity. Set
up a new plate and repeat the reaction.
See
Troubleshooting Sanger sequencing data
User Bulletin (Pub. No. MAN0014435).
The Hi
‑
Di
™
Formamide used to
prepare the samples was
degraded.
Prepare the samples with fresh Hi
‑
Di
™
Formamide and repeat the experiment.
See “Sample preparation guidelines“ on
The sample was prepared with
the BigDye XTerminator
™
Purification Kit but a BDX run
module was not selected.
Re-inject the sample with the correct module.
The sample was degraded.
Prepare the sample according to the protocol
provided with the kits for sample preparation.
See “Sample preparation guidelines“ on
page 37 for sample preparation guidelines.
IMPORTANT!
Do not resuspend samples in
water.
Appendix A
Troubleshooting
Sample and data troubleshooting
A
SeqStudio
™
Genetic Analyzer Instrument and Software User Guide
175
