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We are dedicated to your success. Get back on track. View our expert recommendations for commonly encountered problem scenarios.
View the relevant questions below:
The SeqStudio cartridge has only been tested at the recommended storage conditions (2-8 degrees C). If storing the cartridge on the system, make sure that the Cathode Buffer Container is present and that the power to the instrument remains on.
The SeqStudio cartridge has only been tested at the recommended storage conditions (2-8 degrees C).
The red results indicator on the SeqStudio Genetic Analyzer can mean multiple things relating to the data quality (e.g., offscale signal, no signal, migration issues). More details about each of the issues and how to troubleshoot them are available in Appendix A of the SeqStudio Genetic Analyzer Instrument and Software v.1.1 User Guide.
When the hard drive on the SeqStudio Genetic Analyzer starts to get full, it will automatically delete the oldest run still on the system to make room for the new data.
If you have a Thermo Fisher Cloud account and connect the SeqStudio Genetic Analyzer to it, it is possible to monitor your runs remotely through the SeqStudio app. To set it up:
NOTE: If you are logged into the local account instead of your Thermo Fisher Connect account, these options will not be active.
Here are possible causes and solutions:
The Basecalling Quality alert is triggered when the software is unable to basecall the data due to poor data quality. Re-injecting the sample will sometimes resolve the issue. If it does not, prepare a fresh sample. If the problem persists, please contact Technical Support at techsupport@thermofisher.com.
The reasons that the RFID tag on the consumables may not be recognized are:
Check the labels on the cartridge and Cathode Buffer Container to make sure they are not damaged. Try to re-seat the consumables making sure that the cartridge has clicked into place after insertion and that the Cathode Buffer Container is firmly seated in the autosampler. If the error persists, insert consumables that have previously worked on the system. If the system recognizes these, please contact Technical Support. If the system does not recognize these, please contact Instrument Services to open a service call.
If you get a low QC flag on the SeqStudio Genetic Analyzer, it’s due to either weak signal or no signal being present in the sample. Possible reasons for this are:
Re-running the samples will sometimes improve the results. Before doing so:
After checking the above, if the samples are still not present, try to run the Sequencing Standard control. If the signal is present, then the issue is most likely in generating the template DNA or the sequencing reaction. If the signal is not present, then try to replace the cartridge and re-run. If that fails, please contact Instrument Services as a service call will be required.
The QC flag for high signal strength on the SeqStudio Genetic Analyzer means that some of the peaks reached saturation (>30,000 rfu). Re-injection of the sample will sometimes fix this. If it does not, here are other potential fixes:
Samples showing poor resolution or loss of resolution on the SeqStudio Genetic Analyzer may have degraded over time. Samples are stable in Hi-Di Formamide for up to 24 hours on-instrument. If using the long run module, please limit the run to 48 samples to avoid degradation. If the samples are degrading faster than that, please ensure that the Hi-Di Formamide is less than a year old and has not gone through the freeze-thaw process more than 8 times. If using an injection solution other than BigDye XTerminator or Hi-Di Formamide, try switching to one of them for the injection solution. If the cartridge is past its expiry date, place a new cartridge on the instrument. Sample cleanup can also be a cause for poor data quality or loss of resolution.
Samples showing pull up/pull down in the SeqStudio Genetic Analyzer data could be due to:
The automated spectral calibration algorithm requires high quality data in order to generate an optimized matrix. For fragment analysis, we recommend making a spectral using matrix standards prior to running the first sample. This only needs to be performed once before the initial run. If the spectral was just performed and passed, open the plate setup and verify that the correct dye set was selected for the run.
The sequencing data from the SeqStudio Genetic Analyzer needs to be analyzed in Sequencing Analysis v.6.2 or later. If you currently have Sequencing Analysis v.6.0 software, you may download the latest version by going here.
The sequencing data from the SeqStudio Genetic Analyzer needs to be analyzed in SeqScape Software v.3.1 or later. If you currently have SeqScape Software v.3.0, you may download the patch by going here.
The sequencing data from the SeqStudio Genetic Analyzer needs to be analyzed in Variant Reporter v.2.1 or later. If you currently have Variant Reporter v.2.0 software, you may download the patch by going here.
The Fragment Analysis data from the SeqStudio Genetic Analyzer needs to be analyzed in GeneMapper Software v.5.1 or later. If you currently have GeneMapper Software v. 5.0, you may download the patch by going here.
For Research Use Only. Not for use in diagnostic procedures.