Search

  • Contáctenos
  • Orden Rápida
Ion PI™ Hi-Q™ Chef Kit for Agrigenomics - FAQs

Ion PI™ Hi-Q™ Chef Kit for Agrigenomics - FAQs

View additional product information for Ion PI™ Hi-Q™ Chef Kit for Agrigenomics - FAQs (A43729)

31 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.

For how long is the initialization stable on the Ion Proton Sequencer with the Ion PI Hi-Q sequencing chemistry?

The initialization is stable for 24 hours after initialization. However, we still recommend that you begin the second sequencing run right after the first run is completed.

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

What are some of the improvements seen with the Ion PI Hi-Q Chef workflow over the Ion PI IC 200 Kit?

The main improvements are:

- Higher sensitivity due to improved templating reaction conditions and improved amplification efficiency, especially of GC-rich regions
- Higher specificity and higher amplicon end-to-end sequencing due to the novel Ion Hi-Q sequencing enzyme
- Reduction in hands-on time by 45 minutes due to the pretreatment of the Ion PI Chips v3 in manufacturing
- Over 60% reduction in input DNA required for templating
- Two sequencing runs per initialization

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

Which components should I expect to receive when I order the Ion PI Hi-Q Chef Kit (Cat. No. A27198) or Ion PI Hi-Q Chef Kit for Agrigenomics (Cat. No. A43729)?

The components are listed below:

- Ion PI Hi-Q Chef Supplies: 4 boxes
- Ion PI Hi-Q Chef Solutions: 4 cartridges
- Ion PI Hi-Q Chef Reagents: 4 cartridges
- Ion Proton Sequencing Supplies: 1 box
- Ion PI Hi-Q Sequencing 200 Solutions: 1 box
- Ion PI Hi-Q Sequencing Nucleotides: 1 box

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

I have some Ion PI Chips v2. Is it okay if I use them with the Ion PI Hi-Q Chef Kit chemistry?

No. The Ion PI Chips v2 are not optimized for use with the Ion PI Hi-Q Chef Kit chemistry. We recommend using the Ion PI Chips v3, which have been pretreated during manufacturing and optimized for use with the Ion PI Hi-Q Chef Kit chemistry.

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.

How do I update my Ion Torrent Ion Proton System to the latest software version?

Firmware updates for Ion instruments are included with the latest version of Ion Torrent Torrent Suite Software. First, download and install the latest version of Torrent Suite Software on your Torrent Server. Once completed, your Ion Proton System should alert you that an update is available. You can also start the update process from the Options menu. From the main menu, select “Options,” then “Updates,” “Released Updates,” and “Check.” Once your Ion Proton System has detected the update, press the “Update” button to begin the process. Instructions to update the Ion Proton Sequencer can also be found in the Appendix of the Ion Proton Sequencing Kit user guides.

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 getting the "Chip is not ready/Chip Types do not match" error message with my Ion Proton System. What should I do?

After inserting a new chip and prior to pressing the “Next” button, please wait until a green check mark is displayed on the bottom left of the instrument screen. This indicates that the chip is detected.

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

I'm getting the "FPGA or CPU temp above threshold" error message with my Ion Proton System. What should I do?

This may indicate a fan failure inside the instrument. Please call 1-87-SEQUENCE to open a service call.

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.

Can I use an Ion PI v2 chip for initializing a run using Ion PI Hi-Q sequencing chemistry?

Yes, an Ion PI v2 chip can be used for the initialization. Ensure that the Ion PI Hi-Q initialization program is selected, and an Ion PI Chip v3 is used for the sequencing run.

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

Is the Ion PI Chip v2 compatible with Ion PI Hi-Q sequencing chemistry?

No, the Ion PI Hi-Q sequencing chemistry is only compatible with the Ion PI Chip v3. Using the Ion PI Chip v2 will result in lower loading and data throughput.

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.

I am using the Ion Chef System. The chip/chip adapter does not fit into the chip bucket. What should I do?

Please ensure that you are using the universal chip bucket. Universal chip buckets have an etching on the corners indicating the chip barcode position. If you do not have the universal chip bucket, please call technical support at 1-87-SEQUENCE.

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

I am getting consistently low loading from the same chip position with the Ion Torrent Ion Chef System. What should I do?

The Ion Chef robot arm may need recalibration. Please call 1-87-SEQUENCE to open a service call.

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

I chose the "Pause" option for my Ion Chef system run, in order to collect the QC samples prior to enrichment. After resuming the run, how long do I have until the run completes?

The run should be completed in approximately 1 hour.

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

What is the run time for the Ion Chef instrument?

The run time is approximately 10.5 hours for 200-base read sequencing and about 14 hours for 400-base read sequencing.

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

What is the difference between the "Time" and "Pause" run options in the Ion Chef instrument setup?

The Ion Chef instrument provides two options for obtaining quality control (QC) samples that can be used to assess templating efficiency. Depending on your selection, the QC samples will be made available either during or after the run. In either case, you can obtain unenriched samples from the corresponding Library Sample Tubes at Positions A and B on the Ion PGM Hi-Q Chef Reagents Cartridge, or enriched samples from Positions A and E on the Enrichment Cartridge v2.

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

I am only running one chip on the Ion Chef instrument. Does the instrument only use half of the reagents and can I reuse them?

No, the Ion Chef instrument utilizes all of the reagents in each run regardless of the number of chips being prepared, therefore we recommend always preparing two chips to maximize the throughput of the Ion Chef instrument.

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

What is the Ion Torrent Ion Chef system?

The Ion Chef System simplifies the workflow for Ion PGM, Ion Proton, and S5 systems, providing an automated, high-throughput research solution for reproducible template preparation and chip loading. It can also perform automated library construction for certain Ampliseq panels. For more information, see this link (https://www.thermofisher.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/prepare-template/ion-torrent-next-generation-sequencing-ion-chef-system.html?icid=fr-ionsample-3).

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