Ion PGM™ Dx System - FAQs

View additional product information for Ion PGM™ Dx System - FAQs (A25511)

15 product FAQs found

What should I do if W1 fails at Raw Traces and the screen turns red during the last step of initialization of my Ion PGM System?

The pH of W1 may be out of range or the volume of W1 may be too small or there may have been a minor problem during measurement. Check the amount of W1, press the 'Start' button on the screen, and restart the measurement. If it passes, continue to start the run. If an error appears again, please note the pH of W1, the amount of W1, as well as the error message, and contact Technical Support.br/>
Please note that passing pH values for the reagents may vary depending on the sequencing kit used, but the instrument will automatically determine the correct pH range depending on the sequencing kit selected during initialization. If you are performing the reagent check outside of the initialization, please contact Technical Support for guidance.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

What are the types of next-generation sequencing data files and which should be archived?

Signal Processing Input - Required to reanalyze an Ion Torrent Ion PGM or Ion Torrent Ion Proton run from scratch. (The Output file category is also required).

Basecalling Input - Required to re-analyze an Ion PGM or Ion Proton run from basecalling. (The Output file category is also required).

Output - Required to see the run report in the Torrent Browser and either to reanalyze the run or to launch a plugin.

Intermediate - Useful to troubleshoot a run. Not required for the run report or for re-analysis.

Intermediate files can be deleted if not needed for run troubleshooting. Depending on your institution, you may need to keep all other files (Signal Processing, Basecalling, and Output).

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

How do I change the barcoding set used to analyze a next-generation sequencing run?

Follow these steps to change the DNA barcode ID:

- Open a run reports listing in the “Data,” “Completed Runs & Reports” tab.
- In the list view, click the “Edit” button on the right side of the run listing. The Edit Run window opens.
- Click the barcode menu pull-down and choose the correct barcode set. If you have custom barcode sets, your list is different. Click the “Save” button (in the bottom right corner).
- You can now reanalyze the run from the “Data,” “Completed Runs & Reports” tab.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

How do I reanalyze my next-generation sequencing data with a different reference sequence?

Log in to Torrent Browser and click the “Data” tab, “Completed Runs & Reports page”, and find your run name. In the table view, click the “Reanalyze” option in the gear menu on the right of the run entry. The main run analysis dialog opens. Click the “Advanced” button to display the additional run parameter options. Click the “Alignment Reference” pull-down menu and select the reference for this run. (Optional) Change other advanced options if required. (See “Work with Completed Runs” for a description of the advanced fields.) Click the “Start Analysis” button.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Why do I see the sequence GGCCAAGGCG at the beginning of the majority of the reads in my next-generation sequencing data analysis?

The GGCCAAGGCG sequence is part of the RNA library adapter sequence. This sequence can be automatically trimmed by the software by selecting the “RNA_Barcode_None” option under the Barcodes menu. The run can be reanalyzed with the correct barcode settings to trim the adapter sequence. In the future, the “RNA_Barcode_None” option should be selected in the run plan or selected on the instrument prior to starting the sequencing run.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

How do I archive my Ion Torrent sequencing data?

Please refer to the Data Management section of the Torrent Suite Software user guide for your version of software. The user guides can be found here under Documents: https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/next-generation-sequencing-support-center/ngs-software-support.html

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

How do I analyze my Ion Torrent sequencing data?

Primary analysis and secondary analysis of the data is performed by the Ion Torrent Server. Depending on the application, there may be tertiary analysis plugins that can be installed on the Torrent Server. For other applications, such as RNA-Seq, we recommend using third-party software. For more information, please see the Ion NGS Analysis Workflow page (https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-data-analysis-workflow.html).

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Where can I find the user guides and release notes for Torrent Suite Software?

You can find user guides, release notes, and additional information on the Torrent Suite Software here (https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/next-generation-sequencing-support-center/ngs-software-support.html).

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

What is the Ion Torrent informatics workflow?

For more information on the informatics workflow and analysis software, such as Ion Reporter and Torrent Suite, please go to the Ion NGS Informatics workflow page (https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-data-analysis-workflow.html).

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

I'm having problems using an old, used chip, for initialization of my Ion Proton System. Is there anything I can do?

Rinse the Proton chip by pipetting 100 µL of isopropanol into the chip, followed by 100 µL of water. This may remove any bubbles or reside from the chip surface that may cause initialization issues.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

What should I do if an error message, "Calibration FAILED" appears during initialization of my Ion PGM System?

Open the chip clamp and check for any leaks. If you see solution leaking, please remove the chip and clear the solution with a Kimwipe tissue. DO NOT wipe or scrub, as the socket could be damaged. Clean the socket by gently touching it with a damp Kimwipe tissue. Make sure the socket is dry and replace the chip. Press the “Calibration” button to recalibrate the chip. If it fails again, change the chip to a different one. Also, if you are using an Ion 316 chip v2 on a v3.4 or older instrument, the instrument will not recognize the chip.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

What should I do if a "No Connect FTP Server" alert appears on the Ion PGM touch screen?

The Ion PGM System and Torrent Server may not be connected. Please shut down the system and server and reboot them. The server may enter a system check after the reboot, which will take 3-4 hours. If you have a monitor and keyboard connected directly to the Torren Server, you can avoid the system check by pressing “c” on the keyboard.

If there is a reason you cannot reboot the system, you can run the Ion PGM System without connection to the server. The runs will be saved inside the system. For 200 bp sequencing, here is the number of runs that may be saved for these chip types:

Ion Torrent Ion 314 chip: 40 runs

Ion Torrent Ion 316 chip: 6 runs

Ion Torrent Ion 318 chip: 5 runs

The data will automatically transfer to the server after connection.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

What should I do if R1, R2, R2 and/or R4 fails at Raw Traces and the screen turns red during the last step of initialization of my Ion PGM System?

The pH of the nucleotides may be out of range or there may have been a minor problem during measurement. Press the “Start” button and restart the measurement. If it passes, continue to start the run. If an error appears again, please note the pH of R1, R2, R3, and R4, as well as the error message, and contact Technical Support.

Please note that passing pH values for the reagents may vary depending on the sequencing kit used, but the instrument will automatically determine the correct pH range depending on the sequencing kit selected during initialization. If you are performing the reagent check outside of the initialization, please contact Technical Support for guidance.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

How do I evaluate run performance of an Ion Torrent Ion PGM run?

Please refer to the “How to assess a PGM sequencing run report” in the Documents section of the NGS Sequencing Support Center (https://www.thermofisher.com/us/en/home/technical-resources/technical-reference-library/next-generation-sequencing-support-center/ngs-support.html).

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

For my application, what kits do I need for sequencing on the Ion Torrent Ion PGM System?

Please see the Ion PGM System Product Selection Guide (http://tools.thermofisher.com/content/sfs/brochures/Consumables-Product-Selection-Guide.pdf) for a list of available products for the Ion PGM System workflow organized by application.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.