Thermo Scientific appliedbiosystems SeqStudio Flex Series - Sequencing Results and Well Details

Thermo Scientific appliedbiosystems SeqStudio Flex Series

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Sequencing results and well details

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Chapter 7 View results on the instrument

Sequence analysis results

7

176

SeqStudio

™

Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide

Table of Contents

default chapter3
- Table of Contents3
CHAPTER 1 Product Information16
- Product Description16
- Precautions for Use17
- Instrument Components18
- Instrument Interior Components21
- Power and Communication Connections22
- Theory of Operation23
- Preparing Samples23
- Preparing the Instrument23
- During a Run24
- Results24
- Materials for Routine Operation24
- Instrument Consumables Handling, Usage Limits, and Expiration25
- Configuring the Instrument to Prevent the Use of Consumables Beyond25
- Expiration and Usage Limits25
- Important Notice Regarding Use of Consumables that Exceed Supported Limits25
- Buffer Storage, Usage, and Limits26
- Polymer Storage, Usage, and Limits26
- Conditioning Reagent Storage, Usage, and Limits27
- Capillary Array Storage and Usage27
- Hi-DI ™ Formamide Storage and Usage28
- About the Seqstudio ™ Flex Series Instrument Software V1.028
- Profile and Sign in Options29
- Parts of the Software35
- Companion Software49
- Secondary Analysis Software50
- Network Connection Options51
- Network and Password Security Requirements52
- Network Configuration and Security52
- Password Security52
CHAPTER 2 Get Started53
- Sign in53
- Profile and Sign in Options55
- Create a Local Profile (One Time Only)55
- Sign in57
- Switch User or Sign out59
- Sign in (if Another User Is Signed In)60
- Workflow: Create a Plate, Start and Monitor a Run, then View Results62
- Prepare the Instrument64
- Review Upcoming Maintenance64
- Check Consumables Status66
- Check Instrument Status67
- Preheat the Instrument Oven and the Detection Cell68
- Check for Leaks and Spills68
- Check Buffer Fill Levels70
- Replenish Consumables71
- Ensure Proper Installation of CBC Septa71
- Control the LED Light, Speaker Volume, and Screen Brightness72
CHAPTER 3 Prepare the Samples73
- Sample Preparation Guidelines73
- Plate and Strip-Tube Layout75
- Prepare and Assemble Sample Plates76
- Prepare Sample Plates76
- Prepare the Plate Assembly77
CHAPTER 4 Create a Plate File on the Instrument83
- Create, Copy, or Import a Plate File83
- Options for Creating Plate Files83
- Create a Plate File84
- Copy a Plate File85
- Import a Plate File86
- Enter Plate Properties88
- Enter Injection Properties89
- Specify Replicate Injections92
- Enter Sample Names, Sample Types, and Custom Fields93
CHAPTER 5 Create a Plate File in the Plate Manager Software95
- Options for Creating Plate Files in the Plate Manager Software95
- Get Started with the Plate Manager Software (Desktop)96
- About the Seqstudio ™ Plate Manager 2.0 Software (Desktop)96
- Access the Plate Manager Software (Desktop)99
- Parts of the Plate Manager Software (Desktop) Home Screen101
- Connect the Plate Manager Software (Desktop) to an Instrument103
- Get Started with the Plate Manager Software (Cloud)105
- About the Seqstudio ™ Plate Manager 2.0 Software105
- Connect)105
- Access the Plate Manager Software (Cloud)111
- Parts of Plate Manager Software (Cloud) Home Screen112
- Connect Plate Manager Software (Cloud) to an Instrument114
- Set up a Plate File115
- Create or Open a Plate File (PSM File)115
- Enter Plate Properties116
- Enter Sample and Injection Information116
- Save a Plate File119
- Keyboard Shortcuts and Examples121
- Set up Cloud Analysis in the Plate Manager Software (Cloud)124
- Print the Plate Layout125
- Send a Plate File to the Inbox on the Instrument126
- Additional Functions in the Plate Manager Software127
- Load or Download an Example Plate File127
- Specify Replicate Injections (Add Run Module Function)128
- Use the List View in the Plate Tab128
- Define Custom Fields129
- Save a Plate File in CSV Format129
- Export or Download a Plate File in PSM Format129
- Manage the Software131
- Load and Unload a Plate136
- Load a Plate into the Instrument136
CHAPTER 6 Start and Monitor a Run138
- Unload a Plate from the Instrument139
- Link a Plate File and Start a Run140
- Unlink a Plate File144
- Processes that the Instrument Performs During a Run144
- Pre-Run Check Messages and Plate Alerts During a Run146
- Pre-Run Checks When a Plate Run Starts or a Re-Injection or a Cancelled Injection Is Added to the Run Queue146
- Pre-Run Checks before each Injection or When a Paused Run Is Resumed146
- Run Plates with the Automated Barcode Workflow147
- Create the Plate Files before the Barcoded Plates Are Loaded into the Drawer147
- Pre-Run Checks and Plate Alerts in an Automated Barcode Run149
- View Alert and Notification Details149
- Auto-Spectral Calibration During an Injection150
- Auto-Spectral Calibration Overview150
- Auto-Spectral Calibration Requirements151
- Auto-Spectral Calibration Results152
- View Real-Time Results in the Home Screen153
- Pause the Instrument in the Home Screen157
- Use the Run Queue to Monitor a Run on the Instrument160
- Parts of the Run Queue Screen160
- View Real-Time Results in the Run Queue Screen162
- Change the Injection List Order163
- Cancel or Add Injections or Specify Re-Injections in the Run Queue Screen165
- Pause the Instrument in the Run Queue Screen166
CHAPTER 7 View Results on the Instrument169
- Options for Viewing Results on the Instrument169
- View Results for a Completed Run (Run History)170
- Export Results from the Instrument-Results and Data Files, Logs, and Reports171
- Sample QC and Quality Alerts172
- Use the Electropherogram Screen173
- Sequence Analysis Results175
- Parts of the Sequencing Electropherogram Screen175
- Sequencing Results and Well Details176
- Understanding Quality Values (Qvs)178
- Fragment Analysis Results179
- Parts of the Fragment Analysis Electropherogram Screen179
- Fragment Analysis Results and Well Details180
CHAPTER 8 Use the Remote Monitoring Software to Monitor Runs182
- View Results, and Use Cloud Analysis182
- Monitor a Run from the Remote Monitoring Software182
- Open the Remote Monitoring Software from the Plate Manager Software (Cloud)182
- Open the Remote Monitoring Software from the Instrumentconnect Software183
- Parts of the Remote Monitoring Software Home Screen184
- Plate File Requirements for Viewing Analyzed and Cloud Results187
- View Instrument Notifications in Your Thermo Fisher ™ Connect Account188
- Set up Email Notifications from the Instrument189
- View Real-Time Results in the Remote Monitoring Software190
- Sequencing Results192
- Fragment Analysis Results192
- Cancel Injections or Specify Re-Injections in the Remote Monitoring Software192
- Instrument Home Screen193
- Monitor a Run from a Mobile Device193
- Register the Instrument with the Instrumentconnect App193
- Monitor a Run from a Mobile Device195
- View Results in the Remote Monitoring Software198
- View Results for a Completed Run in the Remote Monitoring Software198
- History Tab)198
- Export a Results Report from the Remote Monitoring Software201
- Download Results from the Remote Monitoring Software201
- Viewing Spectral Calibration or Install Run Results in the Remote202
- Monitoring Software202
- Use Cloud Analysis in the Remote Monitoring Software202
- Automated Cloud Analysis with Secondary Analysis Software202
- Workflow: Cloud Analysis203
- Set up Cloud Analysis for a Completed Run in the Remote Monitoring Software205
- Access Cloud Analysis Results from the Remote Monitoring Software207
- Connect210
CHAPTER 9 Use the Instrument with Thermo Fisher211
- Overview of Thermo Fisher ™ Connect Features211
- Administrator Set up for Thermo Fisher ™ Connect211
- Overview of Thermo Fisher211
- User Set up for Thermo Fisher ™ Connect212
- Local Profile and Cloud Profile: When to Use, User Name, and User Initials213
- Sign in to Apps.thermofisher.com and Access the Instrumentconnect Software215
- (Recommended) Link Directly to Your Thermofisher.com Account217
- Link a Local Profile to Your Thermofisher.com Account (One Time)220
- Sign in to the Instrument with a Cloud Profile222
- Re-Link the Instrument to Your Cloud Profile223
- Disconnect the Instrument from Your Cloud Profile224
- Change Your Cloud Profile PIN225
- Set up Email Notifications from the Instrument226
- Tasks for the Cloud Administrator of an Instrument228
- Enable or Disable Thermo Fisher ™ Connect Access on the Instrument228
- (Administrator Only)228
- Thermo Fisher ™ Connect Cloud Administrator Functions229
- Manage the Users and Administrators of Your Instrument229
- Change the Instrument Name in the Instrumentconnect Software230
- Administrator Only)230
- For more Information on Using Thermo Fisher ™ Connect231
- Connect231
- Use Voice Commands231
- Enable (Register) the Voice Command Function231
- Disable the Voice Command Function232
- Use Voice Commands232
- Basic Voice Commands234
- Interactive Voice Command-Start Run234
- Microphone Icon235
CHAPTER 10 Use the Instrument with the Security, Auditing, and E-Signature (SAE) V2.1 Module238
- Overview of the Security, Auditing, and E-Signature (SAE) V2.1 Module Components238
- Configuring the SAE Module and Setting Permissions239
- Functions that Are Not Available When the SAE Module Is Enabled240
- Enable SAE Mode on the Instrument and Specify the SAE Server (Administrator Only)240
- Disable SAE Mode on the Instrument (Administrator Only)243
- Sign in to the Instrument with SAE Enabled244
- Audit Reason Requirements245
- E-Signature Requirements for Starting a Spectral, Install, or Regular Run245
- Signing an Object before a Regular Run Is Started246
- Signing an Object When a Regular Run Is Started247
- Signing During an Automated Barcode Run249
- Displaying Signatures249
- Use the Instrument When the SAE Server Is Offline250
- SAE Error Messages and Actions251
CHAPTER 11 Manage Library Resources on the Instrument252
- Overview of Libraries253
- General Library Procedures255
- Create a New Entry from a Factory-Provided or Locked Entry255
- Lock or Unlock a Library Entry255
- Copy a Library Entry255
- Edit a Library Entry256
- Import a Library Entry256
- Export a Library Entry256
- Filter Library Lists257
- Delete a Library Entry258
- Plate Files Library258
- Plate File Definition258
- Create a Plate File259
- Define Custom Fields262
- Export or Delete a Plate File264
- Import a Plate Setup from a CSV or PSM File264
- Plate File Properties Tab265
- Plate File Plate Tab267
- Plate File Edit Injection Properties Screen268
- Plate File Edit Well Properties Screen (Sample Name Entry)271
- Run Modules Library272
- Run Module Overview272
- Run Module Provided272
- Create a New Run Module272
- Run Module Settings273
- Size Standards Library275
- Size Standard Overview275
- Size Standard Definition Files Provided275
- Create a New Size Standard276
- Modify a Factory-Provided Normalization Size Standard277
- Size Standard Normalization Feature278
- File Name Conventions Library278
- File Name Convention Overview278
- Create a New File Name Convention279
- File Name Convention Settings282
- Injection Protocols Library283
- Injection Protocol Overview283
- Create a New Injection Protocol283
- Injection Protocol Settings284
- Dye Sets Library285
- Dye Set Overview285
- Create a New Dye Set285
- Create a Custom Dye Set286
- Dye Set Settings286
- Analysis Settings Library288
- Analysis Settings Overview288
- Create a New Analysis Settings289
- Analysis Settings-Sequencing291
- Analysis Settings-Fragment Analysis295
- Results Groups Library301
- Results Group Overview301
- Create a New Results Group302
CHAPTER 12 Run Calibrations and Install Checks304
- Run a Spatial Calibration304
- Spatial Calibration Overview304
- When to Perform a Spatial Calibration304
- Perform a Spatial Calibration305
- Evaluate the Spatial Calibration Results306
- Example Spatial Profiles308
- Export Spatial Calibration Results or Report309
- Run a Spectral Calibration310
- Overview of Spectral Calibration310
- When to Perform a Spectral Calibration311
- System Dye Sets Versus Custom Dye Sets312
- Using Bigdye312
- Estimated Spectral Calibration Run Times313
- Prepare for Custom Dye Set Spectral Calibration314
- Prepare for Spectral Calibration314
- Perform a Spectral Calibration316
- View Spectral Calibration Results317
- Example Spectral Calibration Data324
- Export Spectral Calibration Logs or Report325
- View and Export the Spectral Calibration History326
- Perform an Install Run328
- Overview of Install Run329
- When to Perform an Install Run329
- Estimated Install Run Times330
- Prepare for the Install Run330
- Perform an Install Run333
- View Sequencing Install Run Results334
- View Fragment Analysis Install Run Results347
- View, Export, or Delete an Install Run History352
CHAPTER 13 Maintain the Instrument354
- Maintenance Schedule354
- Review Upcoming Maintenance355
- Daily Instrument Maintenance Tasks356
- Monthly Instrument Maintenance Tasks357
- Annual Planned Maintenance Tasks358
- As-Needed Instrument Maintenance Tasks358
- Maintenance Wizard Overview359
- Clean the Instrument361
- Export Consumables Log Files363
- Install Buffers (Wizard)363
- Install the Anode Buffer Container (ABC)364
- Install the Cathode Buffer Container (CBC)367
- Replenish, Change, Flush, and Store Polymer (Wizards)370
- Precautions for Use370
- Replenish Polymer or Change Polymer Type (Wizard)370
- Store Partially Used Polymer371
- Change and Store a Capillary Array (Wizards)371
- Parts of the Capillary Array372
- Install or Change the Capillary Array (Wizards)374
- Store a Capillary Array375
- Maintain the Pump (Wizards)376
- Parts of the Polymer Delivery Pump376
- Avoiding Damage to the Pump Assembly377
- Remove Bubbles from the Polymer Pump (Wizard)377
- Wash the Pump Chamber and Channels (Wizard)379
- Flush the Water Trap (Pump Trap)379
- Shut Down, Move, and Reactivate the Instrument381
- Shutdown the Instrument (Wizard)381
- Move and Level the Instrument381
- Reactivate the Instrument (Wizard)382
- Maintenance Wizard Procedures382
- Change Capillary Array Maintenance Wizard382
- Change Polymer Type (with Change Array Option) Maintenance Wizard394
- Fill Array with Polymer Maintenance Wizard409
- Remove Bubbles Maintenance Wizard409
- Spatial Calibration Maintenance Wizard412
- Replenish Buffers Maintenance Wizard413
- Wash Pump and Channels Maintenance Wizard415
- Replenish Polymer Maintenance Wizard417
- Shut down Instrument Maintenance Wizard420
- Reactivate Instrument Maintenance Wizard427
CHAPTER 14 Manage the Software (Instrument)439
- Connect the Instrument to a Computer or Network (Hardware Connections)439
- Wired and Wireless Network Options439
- Wired and Wireless Network Connections on the Instrument440
- Antivirus Recommendations for Direct Connection of the Computer to440
- The Instrument440
- Connect the Instrument Directly to a Computer441
- Connect the Software to a Network Drive (Software Settings)443
- Determine the IP Address for a Computer on a Network443
- Create Folders and Enable Network Folder Sharing444
- Connect the Instrument to a Network Drive (Software)445
- Manage Sign-In Profiles446
- Local Profile Roles (Standard and Administrator) and Functions446
- Change the Role of a Local Profile (Administrator Only)447
- Edit Your Own Local Profile447
- Delete a Local Profile or a Cloud Profile from an Instrument (Administrator Only)447
- Create a Local Profile (One Time Only)448
- Change Your Own Local Profile PIN451
- Manage Settings452
- Display Instrument Hardware and Software Information452
- Configure Consumables Usage and Warnings (Administrator Only)453
- Set up Email Notifications from the Instrument454
- (Administrator Only)455
- Enable and Set up Demo Mode457
- Enable/Disable the Internal Barcode Reader (Administrator Only)459
- Set the Power Save Duration (Administrator Only)459
- Connect Access on the Instrument460
- (Administrator Only)460
- Manage Instrument Settings461
- Change the Instrument Name (Administrator Only)461
- Manage Date and Time Settings462
- Update the Software (Administrator Only)462
- Manage the Network Configuration (Administrator Only)464
- Select a Language465
- Configure, Check Status, and Cancel Background Exports and Backups465
- Set the Default Save Location for Results468
- Manage Storage Space468
- Automatic File Cleanup (Autopurge)468
- Export Results from the Instrument-Results and Data Files, Logs, and Reports469
- Delete a Run History469
- Back up User Data (Instrument Settings, Library Items, and Results)470
- (Administrator Only)470
APPENDIX A Troubleshooting471
- Troubleshooting Workflow472
- Troubleshooting Resources473
- Use Smart Help to Request Assistance from Technical Support or Instrument Service473
- Start a Remote Support Session475
- Inspect the Data-Troubleshooting Procedures476
- View the Raw Data and the EPT Plot476
- Check Size Standard Quality (Fragment Analysis)476
- Monitoring Software478
- Inspect the Instrument -Troubleshooting Procedures480
- View the Instrument Sensor Details and EPT Plot480
- Check the Pump for Bubbles or Debris480
- Additional Troubleshooting Procedures482
- Export Troubleshooting Logs482
- Check the Position of the Cathode Buffer Container (CBC)483
- Use the Manual Commands Function to Move Instrument Components483
- Proximity Sensor485
- Power off or Power on the Instrument485
- Instrument Interior Components487
- QC Error and Alert Troubleshooting489
- QC Errors-Sequencing and Fragment Analysis489
- QC Errors-Sequencing490
- QC Errors-Fragment Analysis490
- QC Errors-Spectral Calibration (Manual)492
- QC Errors-Sequencing or Fragment Analysis Install Run494
- Cloud Analysis Troubleshooting495
- Consumables Troubleshooting495
- Home Screen and General Instrument Software Troubleshooting496
- Install Run Troubleshooting498
- Instrument Troubleshooting499
- Library Troubleshooting500
- Maintenance Wizard Troubleshooting501
- Plate Troubleshooting501
- Plate File Troubleshooting501
- Plate Manager Software Troubleshooting502
- Remote Monitoring Software Troubleshooting505
- RFID Troubleshooting507
- Run Troubleshooting507
- Plate Alert Troubleshooting507
- Plate Alert Troubleshooting (Automated Barcode Workflow)509
- Run History Troubleshooting511
- Run Queue Troubleshooting511
- SAE Troubleshooting511
- Sample and Data Troubleshooting512
- Sequencing and Fragment Applications513
- Sequencing Applications517
- Fragment Analysis Applications519
- Settings Screen Troubleshooting519
- Sign in Troubleshooting520
- Software Troubleshooting521
- Spatial Calibration Troubleshooting522
- Spectral Calibration Troubleshooting523
- Thermo Fisher ™ Connect Troubleshooting524
- Voice Command Troubleshooting525
APPENDIX B Run Modules and Dye Sets526
- Run Modules, Read Lengths, Size Ranges, and Run Times526
- Dye Sets530
APPENDIX C Instrument Specifications531
- Instrument Dimensions and Clearance531
- Operating Specifications533
- Environmental Requirements533
- Electrical Requirements534
- Wired and Wireless Network Options and Requirements535
- Network and Firewall Requirements536
- Power and Communication Connections537
APPENDIX D Catalog Numbers539
- Plates Bases Retainers and Septa539
- Instrument Consumables540
- Sequencing Analysis Reagents and Consumables540
- Fragment Analysis Reagents541
APPENDIX E Radio Frequency Identification (RFID) Technology542
- RFID Precautions for Use542
- Locations of RFID Read/Write Units543
- RFID Function543
- RFID Specifications544
- RFID Troubleshooting545
- Symbols on this Instrument546
APPENDIX F Safety547
- Standard Safety Symbols547
- Location of Safety Labels547
- Control and Connection Symbols549
- Conformity Symbols550
- Safety Information for Instruments Not Manufactured by Thermo Fisher Scientific550
- Instrument Safety550
- General550
- Physical Injury551
- Electrical Safety552
- Cleaning and Decontamination553
- Instrument Component and Accessory Disposal553
- Laser Safety554
- Safety and Electromagnetic Compatibility (EMC) Standards554
- Safety Standards555
- EMC Standards555
- Environmental Design Standards556
- Radio Compliance Standards556
- Chemical Safety558
- Biological Hazard Safety559
APPENDIX G Documentation and Support560
- Related Documentation560
- Customer and Technical Support561
- Limited Product Warranty561
- Index562

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