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查看更多产品信息 Ion S5™ XL System - FAQs (A27214)
46 个常见问题解答
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.
In cases of shorter than expected library reads, the 3' quality trimming can be turned off to help distinguish short reads originating from the library preparation and short reads resulting from the 3' quality trimming by the Ion S5 XL System (Cat. No. A27214) software.
To turn off the 3' quality trimming:
1. Select Reanalzye for the run of interest
2. Under the Advanced options, on the Start reanalysis from line, select Base Calling
3. In the Basecaller args box, change the --trim-qual-cutoff 15 value to 100
4. The box should now read, “BaseCaller --trim-qual-cutoff 100 --trim-qual-window-size 30 --trim-adapter-cutoff 16"
5. Give the reanalysis report a new name and Select Start Analysis
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
It takes approximately 47 mins to do a "pulse clean",
Go to "System tools" and select "pulse clean". The instrument must already have been cleaned after a run.
Here are the bottle dimensions:
- Length (Metric) 61 mm
- Height (Metric) 131.1 mm
- Width (Metric) 61 mm
The kit contains 2 bottles of Ion S5 2X Cleaning Solution.
Ion S5 2X Cleaning Solution is compatible with GeneStudio S5/GeneStudio S5 Plus/GeneStudio S5 Prime systems and Ion S5/Ion S5 XL systems.
Ion S5 2X Cleaning Solution is used to perform a pulse clean of your Ion S5 Sequencer (GeneStudio S5/GeneStudio S5 Plus/GeneStudio S5 Prime systems and Ion S5/Ion S5 XL systems) to either recover the instrument performance from a diagnosed solid-state buffer leak or perform preventative maintenance if the instrument has not been used for several months.
Yes, you can update it, but a service engineer would have to be called onsite to carry it out.
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You should reanalyze from base calling. If this fails, please contact your local Bioinformatics support.
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Refer to page 313 of the Torrent Suite Software 5.8 manual (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017530_TorrentSuite5.8_UG.pdf) to change a user's password.
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Formats allowed are explained on page 258 of the Torrent Suite Software 5.8 manual (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017530_TorrentSuite5.8_UG.pdf).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Yes, you can get the software from https://github.com/iontorrent/TS and install in another server. Additionally, you can download the TMAP aligner and Torrent variant caller used in TSS, among other software.
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You can find the main changes in each version's release notes available from www.thermofisher.com. For example, release notes from Torrent Suite Software 5.8 version can be found at https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017478_TorrentSuiteSoftware_5_8_ReleaseNotes.pdf. Alternatively, you can look for “torrent suite software release notes” using your search engine.
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A description of parameters in Torrent browser is provided on page 225 of the Torrent Suite Software 5.8 manual (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017530_TorrentSuite5.8_UG.pdf).
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Filtered variants can be found as explained on page 206 of the Torrent Suite Software 5.8 manual (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017530_TorrentSuite5.8_UG.pdf).
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No, it is not possible to downgrade Torrent Suite Software after upgrade.
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Unaligned reads are merged with aligned reads within the output BAM files whenever a reference genome is provided. The unaligned BAM files are deleted to save space.
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This indicates a problem with library or template preparation. We recommend verifying the quantity and quality of the library and template preparations.
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This could be either due to poor chip loading or because Control Ion Sphere particles were not added to the sample. Please confirm that the Control Ion Sphere particles (included in the Ion S5 Installation Kit) were added. If controls were indeed added, contact Technical Support for assistance.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Here are possible causes and recommended actions to take:
Possible causes:
- Clamp not closed
- Chip not properly seated
- Chip damaged
Recommended action to take:
1. Open the chip clamp, remove the chip, and look for signs of water outside the flow cell.
2. If the chip appears damaged, replace it with a new one.
3. Close the clamp, then repeat the Chip Check.
4. If the chip passes, click Next. If the chip fails, replace it with a new chip, then press Chip Check.
5. If Chip Check continues to fail, there could be a problem with the chip socket. Contact Technical Support.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
Here are possible causes and recommended actions to take:
Possible causes:
- Software updates available
- Connectivity issues
- Instrument not detecting required files or hardware
Recommended actions to take:
Click on the red pop-up to see detailed messages.
If a message states "Newer Software Available": IMPORTANT! After updates are installed, the instrument must be restarted.
a. In the Main Menu, select Options>Updates.
b. Select the Released Updates checkbox, then press Update.
c. When installation is complete, follow the onscreen prompts to restart the instrument.
Note: In some cases, the instrument restarts automatically after software installation. If a message states "No Connectivity to Torrent Server", "No Connectivity to ftp server", or "Network Manager not connected", disconnect and re-connect the ethernet cable, confirm that the router is operational, and verify that the network is up and running. For any other messages:
a. Power off the instrument: In the Main Menu, select Tools > Shut Down > Shut Down.
b. Wait 30 seconds, then press the button on the front of instrument to power on the instrument.
c. If the red "Alarms" and/or "Events" message still appears in the main menu, contact Technical Support.
Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.
You can perform one or two runs per initialization depending on the kit you have:
- Ion 510 & Ion 520 & Ion 530 Kit - Chef (1 sequencing run per initialization), Cat. No. A34019)
- Ion 510 & Ion 520 & Ion 530 Kit - Chef (2 sequencing runs per initialization), Cat. No. A34461)
- Ion 540 Kit - Chef (1 sequencing run per initialization), Cat. No. A27759
- Ion 540 Kit - Chef (2 sequencing runs per initialization), Cat. No. A30011
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Unlike the Ion PGM and Ion Proton Systems, the sequencing reagents for the Ion S5 and Ion S5 XL Systems come with a cleaning solution bottle, which the instrument uses to automatically clean itself after each run.
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No, the W2 solution in the Ion S5 and Ion S5 XL Systems is supplied at the correct pH, so the auto pH step is not necessary.
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For 200 bp sequencing, it will yield 10-15 Gb. 400 bp sequencing is not supported on the Ion 540 Chip.
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For 200 bp sequencing, it will yield 3-4 Gb. For 400 bp sequencing, it will yield 6-8 Gb.
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For 200 bp sequencing, it will yield 0.6-1.0 Gb. For 400 bp sequencing, it will yield 1.2-2 Gb.
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We expect that applications currently supported on the Ion PGM and Ion Proton Systems will be supported on the Ion S5 and Ion S5 XL Systems. However, not all applications have been tested or demonstrated yet.
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No, the instrument will give a warning message regarding the expired reagents, but will not prevent you from running the instrument.
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No, the Ion S5 and Ion S5 XL Systems have an onboard air compressor and tank to store pressurized air.
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Initialization takes 35 minutes for both the Ion S5 and Ion S5 XL Systems.
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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.
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.
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.
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.
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
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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).
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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.
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.
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.
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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.
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.
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.
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.
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.