• About this guide
  • Welcome to the Torrent Suite Software Help System
• Introduction
  • User versus Administrator roles
  • Plan a run
  • Register for a new account
• Samples and Sample Sets
  • Enter new sample
  • Create sample sets manually
  • Import samples to create a sample set
    • Example use of a sample set
      • In the sample set
  • Sample attributes
    • Add a sample attribute
    • Hide a sample attribute
    • Sample information
  • Volcabulary and field restrictions
  • Search samples
  • Edit samples
  • Delete samples
  • Sort samples
  • Import samples
• Monitor sequencing runs
  • Monitor current runs
  • Data views for runs in progress
  • Example monitoring metrics
  • Auto Refresh
    • Review the planned run settings
  • Terminate an analysis run
• Plan an instrument run
  • About Planned Runs
  • Differences between templates and planned runs
    • Customizing and editing templates
  • Create a planned run with AmpliSeq DNA template
  • Create a Planned Run with DNA and Fusions templates
  • Plan a run using Human Identification templates
  • Plan a run with RNA Seq templates
  • Plan a run using Generic Sequencing template
  • Copy a template
  • Export a template
  • Import a template
  • Create a template with Ion AmpliSeq.com Import
  • Plan by sample set
    • Include multiple sample sets in one planned run
    • Create a planned run for mixed samples with a template
  • Create multiple planned runs
    • Create multiple planned non-barcoded planned runs
    • Create multiple barcoded planned runs
  • Analyze Ion AmpliSeq on Ion Chef samples
  • Handle a failed analysis run
  • Determine the fault cause
  • Restart a run
  • Realign a run to a different reference genome
    • Reanalyze a run
    • Reference & Barcoding settings
    • Analysis Options
  • Share a Planned Run among multiple Torrent Servers
  • Execute a Planned Run on your sequencer
• Review data
  • Manage completed runs and results
    • Search for a run
    • Reanalyze a run
    • Edit a run plan
    • Add a run to a project
    • Change the Default Alignment Reference
    • Change run metadata
    • Add barcoding to a completed run
    • Edit run metadata
  • Work with analysis files
    • Analysis results file location
    • Log files in the results folder
    • Standard reference file location
  • Work with projects
    • Create and manage projects
    • View the list of projects
    • Add a report to a project
      • Before analysis
      • From a completed run report
      • From an existing project
    • Download a CSV file of metrics
    • Project menus and actions
    • Actions on members of a project
    • About the mark as duplicate reads option
    • Add selected results to another project
    • Remove result sets from project
    • Search for project names
    • Filter by date
      • Sort projects
• Run Reports
  • Introduction
    • Review pre-alignment metrics
    • Review alignment metrics
    • Download results set
    • Manually run a plugin on the run results
    • Review the planned run settings
    • Review the test fragments and their quality metrics
    • Review Chef Summary
    • Review calibration report
    • Review analysis information
    • Review report error log
  • Report header
  • Compare run reports
  • Run report metrics
    • Run metrics overview
    • Predicted quality (Q20)
    • Quality following alignment (AQ20)
      • Aligned read length calculation
      • Alignment
      • Which reads are used in the alignment process
    • Run report metrics before alignment
      • ISP density
        • Key signal
      • ISP summary
      • Read length
    • Run report metrics on aligned reads
      • Total aligned bases
      • Raw accuracy
      • Alignment quality
    • Barcode reports
    • Output files
      • The BAM format
      • FASTQ file format generation
      • Rename your output files
  • Test fragment report
    • Open the test fragment report
    • Test fragment metrics
    • Read length histogram1
  • View Analysis Details of a report
    • Analysis details
    • Software version
    • Support
• Applications
  • Introduction
  • Oncology – Liquid Biopsy
    • Plan an Oncology – Liquid Biopsy run from template
    • Create an Oncology – Liquid Biopsy Planned Run template
    • Review Oncomine cfDNA assay run results
  • 16S Metagenomics application
    • Plan a run using Ion 16S Target Sequencing template
• Plugins
  • Install plugins
    • Enable an installed plugin
    • Uninstall a plugin
  • Plugin configuration
    • Configure plugins globally
  • Set a plugin to run by default after every run
  • Run a plugin manually from the sequencing run report
  • View plugin run status
    • Stop a plugin run
    • Open a plugin log
    • Delete a plugin result
  • Pre-installed plugins
    • ampliSeqRNA plugin
      • ampliSeqRNA plugin configuration
      • Review run results
        • Distribution plots
        • Correlation heatmap
        • Correlation plot
        • Gene heatmap
        • Downloadable reports
    • Assembler SPAdes plugin
      • Assembler SPAdes plugin configuration
      • Review run results — AssemblerSPAdes plugin
    • coverageAnalysis plugin
      • coverageAnalysis plugin configuration
      • Review run results — coverageAnalysis plugin
        • coverageAnalysis plugin report
          • Example statistics
          • Reads statistics 
          • Example charts
          • Output files
    • Data Export plugin
      • Data Export plugin configuration
      • Review run results — DataExport plugin
    • ERCC Analysis plugin
      • ERCC Analysis plugin configuration
      • Review run results — ERCC plugin
        • Interpret the ERCC Dose Response plot 
        • View ERCC transcript details
        • Definitions
      • ERCC resources
    • FieldSupport plugin
    • FileExporter plugin
      • Configure the File Exporter plugin
      • Review run results — FileExporter plugin
    • FilterDuplicates plugin
      • Review run results — Filter Duplicates plugin
    • immuneResponseRNA plugin
      • immuneResponseRNA plugin configuration
      • Review run results — Immune Response plugin
    • IonReporterUploader plugin
    • PGxAnalysis plugin
      • Review run results — PGxAnalysis plugin
    • RNASeqAnalysis plugin
      • RNASeqAnalysis plugin configuration
      • Create an RNA Seq analysis run from factory template
      • Review run results — RNASeqAnalysis plugin
        • Distribution Plots
        • Correlation heatmap
        • Correlation plot
        • Gene heatmap
        • Isoform heatmap
        • Downloadable reports
        • Individual barcode view
          • Downloadable reports
    • RunTransfer plugin
      • RunTransfer plugin configuration
      • Review run results — Run Transfer plugin
    • sampleID plugin
      • Review run results — sampleID plugin
    • variantCaller plugin
• Integration with Ion Reporter Software
  • Transfer limitations
  • Install the Ion Reporter Software uploader plugin on your Torrent Server
  • Set up an account for IonReporterUploader plugin
    • Red status on Ion Reporter Software account configuration page
    • When the IonReporterUploader Plugin is Not Configured
      • In the plugin manual launch page
      • In the run plan template wizard
      • In the plugin configuration page
  • IonReporterUploader plugin configuration
  • Upload to Ion Reporter Software
  • Run IonReporterUploader plugin manually
  • Add Ion Reporter Software to a planned run or run template
    • Manage the Ion Reporter workflow List
    • Sample gender
    • Results files for barcoded sequencer runs
  • Check the Progress of your File Transfer
    • Email notifications
    • Check Plugin Summary for IonReporterUploader plugin status
    • Check IRU status in log file
      • Configuration errors
  • Review run results before automatic upload to Ion Reporter Software
    • Edit run plan template to review results before IRU upload
    • Edit run plan to review results before IRU upload
  • Tune Ion Reporter Uploader speed parameters
  • Torrent Suite Software output and Ion Reporter Software analysis phases
  • View IonReporterUploader plugin usage
    • Delete plugin report files
    • Rescan plugin output files for a specific run
  • Ion Reporter Uploader command-line utility
    • Download Ion Reporter Uploader command-line utility
    • Run Ion Reporter Uploader command-line utility
• Torrent Variant Calling
  • Introduction
    • Supported Ion AmpliSeq panels
  • Run the variantCaller plugin
    • Configure the variantCaller plugin in a template or run plan
    • Run the variantCaller plugin manually
    • Barcode-aware Torrent Variant Calling
      • the variantCaller plugin manual launch for custom configuration per barcode
      • Apply variantCaller plugin settings to all barcodes
      • Modify and apply the variantCaller plugin settings for all or select barcodes
      • Add, edit and delete configurations
      • Download files and other actions
      • Export to file
      • Barcoded variantCaller summary area
    • Input
      • Reference
      • Library type
      • Input files
        • Parameter files
        • Target regions and hotspot regions
        • Target regions file
        • Hotspots file
  • Output from the variantCaller plugin
    • Review run results — variantCaller
    • Run report plugin summary
      • Barcoded variantCaller summary area
      • Non-barcoded variantCaller summary area
    • Variant Caller Report
      • Buttons for downloads and other actions
    • Variant Calls by Allele table
      • View Allele Annotations 
      • View Coverage Metrics 
      • View Quality Metrics
      • Export to file
  • Troubleshoot the variantCaller plugin results
    • Find False Negatives
    • Fix False Positives
    • Contact Field Bioinformatics Specialist
    • Rerun the variantCaller plugin
  • Parameter Settings defaults
  • About the use of Variant Caller Parameter Settings radio buttons
  • Upload your custom parameter values
  • variantCaller plugin configuration
    • Variant Caller parameters
      • the variantCaller plugin main parameter settings
      • Advanced settings
        • Long indel assembly advanced settings
        • FreeBayes advanced settings
• Reference Management
  • GRCh38 human reference
    • Add the Ion GRCh38 Reference to Torrent Suite Software
  • AmpliSeq Designer preloaded reference genomes
  • References Management Guide
    • Rebuild warning
    • Reference pages
    • Upload a new reference file
    • Prerequisites
    • Import preloaded ion references
    • Import custom reference
    • Error handling
    • Target Regions Files and Hotspot Files
    • Details page
      • File details and download
      • Zip file details and download
      • Upload log file
  • Manage Target Regions Files and Hotspot Files
    • Overview
    • Summary of steps to add a target regions or hotspots file
      • Modify a BED file
      • Supported file types
      • Upload a BED or VCF file
      • After upload
      • Uploading errors
    • Download a hotspots or target regions file
    • Delete a hotspots or target regions file
    • BED File Formats and Examples
    • Target Regions File Formats
      • 3-column Target Regions BED File Format
      • 4-column Target Regions BED File Format
      • 6-column Target Regions BED File Format
      • 8-column Target Regions BED File Format
      • BED files generated by AmpliSeq.com custom designs
    • HotSpots File Format
      • The HotSpotAlleles field
      • Partial example of a HotSpots BED file
      • Extended BED Detail format
      • Examples from BED files in the Extended BED Detail format
      • Merged Extended BED Detail format files
        • Example 1
        • Example 2
      • The score and strand fields in uploaded BED files
    • RNA Fusions BED File Formats and Examples
      • Track line
      • Example BED file entries
    • Manage DNA Barcodes and DNA Barcode Sets
      • Access the DNA barcode set pages
      • Pre-installed DNA barcode sets
      • View a DNA barcode or barcode set
        • IonSet1 barcodes
        • IonXpress barcodes
        • IonXpressRNA barcodes
        • RNA_Barcodes_None barcode
          • Museek barcode
        • For custom DNA barcode sets
          • Add a custom DNA barcode set
          • Delete a DNA  barcode set
          • Add a barcode to an existing DNA barcode set
          • Delete an individual barcode
          • Edit an individual barcode
        • Update Reference Library Indices
      • Work with Test Fragments
        • Edit a test fragment
        • Add a test fragment
      • Download an Ion Reference File
        • Download a reference file
    • Details about the Ion hg19 Reference
      • Three positions with ambiguity codes
      • Hard masked PAR regions in chromosome Y
      • Chromosome M
      • Work with Obsolete Reference Sequences
        • Why are my references obsolete
      • Delete a Reference Sequence
        • Delete a Reference Sequence
• Data Management
  • Data management
    • Disk space monitoring
      • Configure notifications for low disk space
      • Data management rule configuration
      • Check disk usage
      • Graph usage indicators
      • Usage totals
      • Error messages
      • Disk full messages
    • Configure automatic data management
      • Enable automatic archives of run data
      • Enable automatic deletion of run data
    • Data import
    • Export run data
    • Active data management jobs
      • Category statistics
    • Disk Space Management
    • Auto refresh runs and results
    • Category statistics
    • Manage data for selected run reports or run projects
      • Delete, archive, or export run data
      • Delete run data
      • Archive run data
    • View the Data Management log
    • Increase file storage and available disk space
      • Mount a USB drive
        • Mount a USB drive
        • Unmount a USB drive
      • Connect to a Torrent Storage NAS device
        • Connect directly to Torrent Storage NAS device
        • Connect over a network to a Torrent Storage NAS device
      • Monitor the Torrent Storage NAS device
• Software administration
  • Torrent Suite Software updates
    • Update Torrent Suite Software
    • Lock current Torrent Suite Software version
    • Enable off-cycle product updates
    • Update off-cycle release plugins
    • Manage Torrent Suite Software user accounts
      • Add a user account
      • Modify a user
      • Delete a single user account
      • Delete multiple user accounts
      • Approve requests for new accounts
      • Torrent Suite Software user password changes
        • Create a new superuser account to change a password
        • Change a password in the Torrent Suite Software database
      • Check user account notification
      • Approve and reject new accounts
  • Disk usage
  • Add customer support contacts
  • Change the displayed server name
  • Change the time zone for the Ion Torrent Server
  • Monitor your Ion Torrent Server
    • Jobs Server service
    • Start a job request
    • Stop a run that is in progress
    • ionCrawler service
    • RAID Info
  • Set up Ion Mesh
  • View network settings
  • Data backup and restore locations
    • Restore the PostgreSQL Database
  • Axeda Remote System Monitoring (RSM)
    • Overview
    • Port assignments
    • Data automatically collected by the RSM agents
    • Torrent Server
    • Ion PGM data
    • Ion S5 and Ion Proton data
    • Remote access for troubleshooting
  • Troubleshoot Torrent Server
    • Check crawler and job server status
      • Queue status
    • Restart services
    • Verify network connectivity and name resolution
    • Verify Torrent Server IP address
    • Troubleshoot and configure the time service
    • Verify file transfer
    • Further investigation and problem resolution
    • Customer support archive
      • Generate a Customer Support Archive
      • Customer Support Archive contents
    • View system support diagnostics
    • View instrument diagnostics
  • Administration with command-line utilities
    • Monitor disk space
    • Change the hostname
    • Change the time zone
    • Add an HTTP proxy
    • Alternate checks
• Manage sequencer settings from Torrent Suite Software
  • Work with analysis files
    • Analysis results file location
    • Log files in the results folder
    • Standard reference file location
  • Design custom barcodes
    • Cautions
    • Barcode overview
    • Barcode set design considerations
    • Hamming distance
    • Ternary encoding
    • Ion Torrent barcode design
  • Scan your sequencing kit
    • The template wizard
  • Use DNA barcodes with the Ion Torrent Sequencers
    • Overview
    • Workflow
    • Summary of the recommended workflow
    • Set up a barcode run in a template
    • Start your planned run on the Ion sequencer
    • Start your planned run on the Ion S5 or Ion S5 XL sequencer
    • Other methods to import your planned run
      • Planned run run code
    • Barcode reports and output files
    • Plugin Support for Barcodes
  • Reference library and barcode
  • Connect the sequencer instrument to the Torrent Server
  • Default settings for experiments
    • Open the Site Administration screen
      • Change the report name
      • Change the run date
  • Update the Ion Ion OneTouch Device
  • Update Ion Chef scripts
  • Handle a failed analysis run
    • Determine the fault cause
• Screen descriptions
  • Planned Runs screen
  • Samples screen
  • Templates screen
  • Planned Run List screen
  • Runs in Progress screen
  • Ion Chef screen
  • Completed Runs & Results screen
  • Run Report
  • Projects screen
  • Data Management screen
  • Analysis Parameters screen
  • References screen
  • Services screen
  • Plugins screen
  • Ion Reporter configure screen
  • Configure screen
  • Account Settings
  • Product and Plugin updates
• Barcoded libraries
  • Pre-installed barcode sets
  • Select a barcode set for a sequencing run
  • Custom barcode sets
    • Create and add a custom barcode set on the Torrent Server
    • Other barcode set operations
      • View a barcode set
      • Delete a custom barcode set from the Torrent Server
      • Add a barcode to a custom barcode set
      • Edit or delete a barcode from a set
• Reference
  • Wizard Plan or Save step in the Workflow bar
  • Wizard Ion Reporter Page
  • Wizard Application Page
  • Wizard Kits Page
    • Base Calibration mode options
  • Wizard Plugins Page
  • Wizard Projects Page
  • Templates 
    • Plan > Template screen organization
    • Template customization
    • Plan > Template screen organization
  • Plan Tab
    • Planned Runs 
      • Wizard
        • Start the wizard
          • Wizard Ion Reporter Page
          • Wizard Application Page
          • Wizard Kits Page
          • Wizard Plugins Page
          • Wizard Projects Page
            • Wizard Plan or Save step in the Workflow bar
    • Example Planned Runs page
  • CSV Metrics File Format
  • Per-Base Quality Score System
    • Quality Score Predictors
  • Ion Torrent BAM format
    • Custom SAM Recorder Tags
  • Dataflow file sizes
    • Torrent Suite Software 5.2/5.0 and 400 bp kit on the Ion S5 XL System
    • Ion Proton dataflow with 4.x software and 400 bp kit
    • Ion Proton dataflow with 4.x software and 200 bp kit
  • Configure and select a custom analysis parameter set
    • Find the TMAP command for a specific analysis
  • The Command Line Args (Advanced) tab
  • Overview of BaseCaller and Barcode Classification
    • About barcodes
    • Analysis pipeline overview
    • Overview of BaseCaller functionality
      • Notes about barcode classification and barcode filtering
    • Troubleshooting Barcode Classification Issues
    • Explanation of fields in the BaseCaller JSON file
      • Read count
      • Filtered
      • Barcode errors histogram
      • Barcode distance histogram
      • Barcode match filtered
      • Barcode bias
  • BaseCaller arguments
    • BaseCaller Parameters
    • Barcode classification parameters
    • The cutoff setting
    • The separation setting
    • Other public parameters
    • Examples of BaseCaller parameters usage
  • TMAP Modules
    • Mapping modules
    • Find the TMAP command for a specific analysis
    • TMAP examples
    • Global options used by all TMAP modules
    • Global pairing options
    • TMAP map1 Options
    • TMAP map2 Options
    • TMAP map3 Options
    • TMAP map4 Options
    • TMAP mapvsw Options
• Legal