Bulletins 7

Local Run Manager 2: How to use a custom library prep kit
Local Run Manager: Generate FASTQ files from an incomplete run
FASTQ files explained
Upgrading from bcl2fastq to BCL Convert
How to connect benchtop instruments and Local Run Manager to a network location
Why is allowing mismatches when demultiplexing desirable?
Troubleshooting demultiplexing issues using Local Run Manager
Local Run Manager: How to requeue and import run data for reanalysis
What sequences do I use for adapter trimming?
TruSight™ Oncology 500 Assays and Analysis Options
BaseSpace Sequence Hub server instances explained
How to use BaseSpace CLI to upload FASTQs to BaseSpace Sequence Hub
How to edit a sample sheet and requeue an analysis in BaseSpace Sequence Hub

Index

NextSeq 500-550 Self-Service
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Contents - 1 General Use
Contents - 2 Setting up a run
Contents - 3 Instrument maintenance
NextSeq 500/550 Troubleshooting 1
NextSeq 500/550 Troubleshooting 2
NextSeq 500/550 Troubleshooting 3
NextSeq 500/550 Troubleshooting 4
Section 3: Additional Resources
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Section 1: General Use
Section 1: General Use
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Section 1 contents - Preparing for a run
NGS for beginners
Indexing Considerations for the NextSeq 550 Samplesheet & Maximum read lengths and number of cycles
Networking Illumina® Benchtop Instruments with Windows 10 OS
Cluster density guidelines for the NextSeq 500/550
Choosing a library Loading concentration for Illumina sequencing
Optimal Cluster Density Best Practices
Sequencing: Considerations for Low Diversity Libraries
How to use the Illumina® Sequencing Coverage Calculator
Run Setup Modes for NextSeq 500/550
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Section 1 contents - Setting up a run
Preparing reagents pre-run
Denature and Dilute Libraries
How to set up a PhiX validation run
How to Select Custom Recipes on the NextSeq 550 in NCS 4.0.X
How to Skip the Pre-Run Check Confirmation on the NextSeq 550
Library pooling guidelines for the NextSeq systems
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NextSeq 500/550 instrument maintenance
How to set up a wash on the NextSeq 500/550
How to clean Illumina NGS sequencer wash cartridges
How to power cycle and reboot the NextSeq 500/550
Run folder sizes and Disk Space on the NextSeq 500/550
How to enable Proactive on the NextSeq 500/550
Best practices for maintaining the computer on a NextSeq
How to perform a System Check on the NextSeq 500/550
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How to Create LRM Credentials to Perform a NextSeq 550 System Check in NCS 4.0.X
Waste Volumes for NextSeq 550 Reagents
Post-Run Automatic Purge for NextSeq 550
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Section 2: NextSeq 500/550 Troubleshooting
Section 2: NextSeq 500/550 Troubleshooting
Contents NextSeq Troubleshooting 1
Contents NextSeq Troubleshooting 2
Contents NextSeq 500/550 Troubleshooting 3
Contents NextSeq 500/550 Troubleshooting 4
Troubleshooting RFID errors on the NextSeq 500/550
Troubleshooting a Full Spent Reagents Cartridge warning on the NextSeq 500/550
Troubleshooting NextSeq 500/550 (NCS 2.2.0 or earlier) not showing Planned Run from BaseSpace PrepTa
Troubleshooting Lane Pump not initialized
Troubleshooting Local Run Manager analysis module not available at run start on NextSeq 500/550
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Troubleshooting Initialization Failure due to Proxy Warning on the NextSeq 500/550
Troubleshooting Flow Cell Registration Failure (Fiducial Error)
Troubleshooting issues unloading reagents on a NextSeq 500/550
Troubleshooting Failed Camera Board on the NextSeq 500/550
Troubleshooting Custom Sequencing Primers selected by mistake during setup in manual mode
Troubleshooting Cannot Update Metrics errors on the NextSeq 500/550
Troubleshooting Error Related to InstrumentMaintenanceState.xml
Troubleshooting Bit Error check failures on the NextSeq 500/550
Troubleshooting Blank BaseSpace Login Screen During Run Setup for NextSeq 500/550
Troubleshooting an Object Reference Error on the NextSeq 500/550
Troubleshooting An existing connection was forcibly closed by a remote host error on the NextSeq 500
Troubleshooting Bad Request error in NextSeq’s Local Run Manager
Troubleshooting an Imaging Limits Pre-Run Check Error on the NextSeq 500/550
Troubleshooting a NextSeq 500/550 Universal Copy Service Error (NCS 4.0+)
Troubleshooting a RAID warning on the NextSeq 500/550
Troubleshooting a RheodyneValve Error on NextSeq 500/550
Troubleshooting a stuck Buffer Cartridge/Tray in the NextSeq 500/550
Troubleshooting Access to the path 'C:\NextSeqCalibration.cfg' is denied error on NextSeq 500/550
Troubleshooting a NextSeq 500/550 Cavro Syringe Pump Error
Troubleshooting a Flow Cell Door Error on the NextSeq 500/550
Troubleshooting a Flow Cell Registration Failed (Skew) Warning on the NextSeq 500/550
Troubleshooting a Flow Cell Registration Stall During Pre-Check on First Run after NextSeq 500/550
Troubleshooting a Fluidics Automation Error on the NextSeq 500/550
Troubleshooting a Failed to Get Temperature warning on the NextSeq 500/550
Troubleshooting a "Would you like to include the first time setup results with this run?" notificati
Troubleshooting a “Not Found” Error Message on a NextSeq 500/550
Troubleshooting Software Shutdown Issue Warning on the NextSeq 500/550
Troubleshooting “My Output Folder is Empty” on NextSeq 500/550 NCS 4.0
Troubleshooting a Camera Disabled: Failed to Detect Clusters error for a sequencing run that does no
Troubleshooting Cycle 1 Error on the NextSeq 500/550: Camera Disabled: Failed to Detect Clusters
Troubleshooting Wash State Unknown in NextSeq 500/550 (NCS 4.0.0)
Troubleshooting NVRAM or Socket Error on NextSeq 500/550
Troubleshooting No Run Folder Created in NCS 4.0 when output folder is set in Local drive
Troubleshooting NextSeq 500/550 Async Command Timeout Error
Troubleshooting Possible Stale or Saturated Image Data Detected on the NextSeq 500/550
Troubleshooting presence of snr.csv files in Temp folder on NextSeq 500/550 (NCS 4.0.2)
Troubleshooting a Remote Server Error on NextSeq 500/550
Best Practices for NextSeq 500/550 Pre-Run check failures requiring a power cycle
Section 3: Additional Resources
Section 3: Additional Resources
How To's & Further Resources 1
How To's & Further Resources 2
Bulletins 1
Bulletins 2
Bulletins 3
Bulletins 4
Bulletins 5
Bulletins 6
Bulletins 7
Bulletins 8
Bulletins 9
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Technical & Application Notes - 1
Technical & Application Notes - 2
Webinars & Trainings - 1
Webinars & Trainings - 2
How many cycles of SBS chemistry are in my kit?
Online Tools
Online Tools 2
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Order the NextSeq 550 system and reagent kits
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Feedback
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Back cover