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Torrent Suite Software 5.12 Help

Contents

  • Introduction to Torrent Suite Software
    • Torrent Suite Software product information
    • Operating system compatibility
    • Browser compatibility
    • Hardware compatibility
    • Network and password security requirements
      • Network configuration and security
      • Password security
  • Get started with Torrent Suite Software
    • Dashboard at a glance
    • News screen
    • User (Staff) versus Administrator (Superuser) roles
    • Plan a run
    • Register for a new user account
  • Samples and Sample Sets
    • About samples and Sample Sets
    • Create a Sample Set manually
    • Create a Sample Set by importing samples from a CSV file
    • Create a samples file from a template
    • Sample information
      • View Sample Set attributes
      • Add a sample attribute to a sample
      • Manage sample attributes
      • Sample attributes
      • Sample Set definitions
    • View Ion AmpliSeq library preparation on an Ion Chef System run
    • Find a Sample Set
    • Sort Sample Sets
    • Edit a Sample Set
    • Delete a Sample Set
    • Create an Ion AmpliSeq on Ion Chef Sample Set
  • Plan and execute an instrument run
    • Planned Runs
    • Planned Run templates
      • Planned Run templates for specific research applications
      • Create a custom Planned Run template
      • Create a Planned Run from a Planned Run template
      • Create a Planned Run without a Planned Run template
      • Search for a Planned Run template
      • Export a Planned Run template
      • Import a Planned Run template
      • Save a Planned Run template to Favorites
    • Steps in the workflow bar
      • Ion Reporter step in the workflow bar
      • Research application step in the workflow bar
      • Kits step in the workflow bar
        • Advanced Settings—Kits step in workflow bar
        • About the Mark as Duplicates Reads option
      • Plugins step in the workflow bar
      • Projects step in the workflow bar
      • Plan step in the workflow bar
    • Review Planned Run settings
    • Import panel files and parameters
      • Link your Ion Torrent Server account to AmpliSeq.com
      • Import Planned Run template parameters
      • Manually upload panel files
      • Copy an analysis parameter set
    • Create Planned Runs
      • Plan by Sample Set
      • Create a Planned Run with Sample Sets
        • Command Line Args (Advanced) screen
      • Create a Planned Run for mixed samples with a Planned Run template
    • Create multiple Planned Runs
      • Create multiple Planned Runs for non‑barcoded libraries
      • Create multiple Planned Runs for barcoded libraries
    • Planned Runs list
      • Manage Planned Runs
      • Planned Run status
        • Manually change Ion Chef Instrument run status
      • Execute a Planned Run on a sequencer
      • Transfer a Planned Run to another Ion Torrent Server
  • Monitor runs in progress
    • Monitor a sequencing run
    • Monitor an Ion Chef run
    • View data for runs in progress
    • Auto Refresh the Monitor tab
    • Review the Planned Run settings
    • Stop an analysis job
    • View system memory usage
  • Review and manage run reports
    • About run reports
    • Search for a run report
    • Open a run report
      • Review unaligned reads
        • Run report metrics before alignment
      • Review aligned reads
        • Quality following alignment
          • Aligned read length calculation
          • Alignment
          • Reads used for alignment
          • Predicted quality (Q20)
            • Per-base quality score system
            • Quality score predictors
        • Run report metrics after alignment
      • Run report metrics
        • Throughput considerations
        • ISP loading density
        • Total reads
          • Well classification
          • Read filtering and trimming
        • Read length
        • Key signal
      • Output files
        • Download output files
        • View and download barcode reports
      • Download a run report summary PDF
    • View details about completed runs
      • View test fragments for a completed run
      • View consumables used in a completed run
      • View the summary for an Ion Chef Instrument run
      • View the calibration report for a completed run
      • View analysis details for a completed run
      • View software versions used in a run
    • Organize run results with projects
      • Search for projects by name
      • Add a project to a Planned Run
        • Add selected results to another project
      • View result sets in a project
      • Compare reports of runs in a project
      • Manage data for result sets in projects
      • Combine aligned reads from multiple run reports
      • Download a CSV file of metrics
        • Analysis metrics file fields
      • Remove a result set from a project
    • Reanalyze a run
      • Change the default alignment reference
    • Edit a run report
      • Add or change barcoding for a completed run report
    • Set the Completed Runs & Reports screen to automatically refresh
  • Manage plugins for data analysis
    • Plugin configuration
      • Configure plugins globally
      • Configure a plugin to run automatically
    • Run a plugin manually from the sequencing run report
    • Download a plugin report PDF
    • View plugin run status
      • Stop a plugin run
      • Open a plugin log
      • Delete plugin results from a run report
      • Rescan a plugin
    • Preinstalled plugins
      • ampliSeqRNA plugin
        • ampliSeqRNA plugin configuration
        • Review ampliSeqRNA plugin results
          • ampliSeqRNA plugin reports
      • AssemblerSPAdes plugin
        • AssemblerSPAdes plugin configuration
        • Review AssemblerSPAdes plugin results
        • Analysis metrics file fields
      • coverageAnalysis plugin
        • coverageAnalysis plugin configuration
        • Review coverageAnalysis plugin results
          • Reads statistics 
          • Example charts generated by the coverageAnalysis plugin
          • Output files generated by the coverageAnalysis plugin
      • DataExport plugin
        • DataExport plugin configuration
        • Review DataExport plugin results
      • ERCC_Analysis plugin
        • ERCC_Analysis plugin configuration
        • Review the ERCC_Analysis plugin results
          • Interpret the ERCC Dose Response plot 
          • View ERCC transcript details
          • Definitions
        • ERCC resources
      • FieldSupport plugin
      • FileExporter plugin
        • Configure the FileExporter plugin
        • Review FileExporter plugin results
      • FilterDuplicates plugin
        • Review FilterDuplicates plugin results
      • immuneResponseRNA plugin
        • immuneResponseRNA plugin configuration
        • Review immuneResponseRNA plugin results
          • Downloadable reports
      • IonReporterUploader plugin
      • molecular Coverage Analysis plugin
        • molecular Coverage Analysis plugin configuration
        • Review molecular Coverage Analysis plugin results
          • Molecule statistics
          • Example charts generated by the molecular Coverage Analysis plugin
          • Output files generated by the molecular Coverage Analysis plugin
      • PGxAnalysis plugin
        • Review PGxAnalysis plugin results
      • RunTransfer plugin
        • RunTransfer plugin configuration
        • Review RunTransfer plugin results
      • sampleID plugin
        • Review sampleID plugin results
      • variantCaller plugin
    • Plugins available on Connect
      • RNASeqAnalysis plugin
        • RNASeqAnalysis plugin configuration
        • Review RNASeqAnalysis plugin run results
          • Downloadable reports for individual RNASeqAnalysis plugin barcodes
          • Individual barcode view
          • Distribution plots
          • Correlation heatmap
          • Correlation plot
          • Gene heatmap
          • Isoform heatmap
      • smallRNA plugin
        • smallRNA plugin
        • Review smallRNA plugin results
  • Variant calls in Torrent Suite Software
    • About the variantCaller plugin
    • Run the variantCaller plugin
      • Configure the variantCaller plugin to run by default after every run
      • Configure the variantCaller plugin to run as part of a Planned Run
      • Run the variantCaller plugin manually
      • variantCaller plugin configuration
    • Create a custom configuration for the variantCaller plugin
    • Apply configuration settings to specific barcodes
    • Create and use a custom parameters setting
    • Review variantCaller plugin run results
      • Detailed variantCaller plugin report
      • Variant Calls by Allele table
      • View allele annotations 
      • View coverage metrics 
      • View quality metrics
      • Export variant calls to a file
      • Troubleshoot variantCaller plugin results
        • Find false negatives with an alignment viewer
        • Find false negatives by using the variantCaller plugin report
        • Fix false positives
        • Export files for troubleshooting
    • Save adjusted parameters to a variantCaller plugin configuration
    • variantCaller plugin advanced parameters
      • Torrent Variant Caller module advanced settings
      • FreeBayes module advanced settings
      • Long INDEL Assembler module advanced settings
      • Advanced argument settings
  • Integration with Ion Reporter Software
    • About Ion Reporter Software
    • Install the IonReporterUploader plugin on a Ion Torrent Server
    • Set up an account for IonReporterUploader plugin
    • Automatically transfer Torrent Suite Software output to Ion Reporter Software
      • Manage the Ion Reporter Software analysis workflow list
      • Sample gender
    • Run the IonReporterUploader plugin manually
    • IonReporterUploader plugin configuration
    • IonReporterUploader plugin file transfer progress
      • View IonReporterUploader plugin status details
      • Delete IonReporterUploader plugin report files
    • Tune IonReporterUploader plugin speed parameters
    • Review IonReporterUploader plugin results
      • Torrent Suite Software output and Ion Reporter Software analysis phases
    • IonReporterUploader command-line utility
      • Download IonReporterUploader command-line utility
      • Run IonReporterUploader command-line utility
  • References management
    • About references
    • Reference sequences
      • hg19 reference
        • Hard masked PAR regions in chromosome Y
        • Three positions with ambiguity codes
        • Chromosome M reference sequence
      • GRCh38 reference
      • Import reference sequence files
        • Guidelines for importing custom reference sequence files
        • Import a preloaded reference sequence file
        • Import a custom reference sequence file
      • View a reference sequence file
      • Edit reference sequence file properties
      • Permanently delete a reference sequence file
      • Obsolete reference sequences
    • Target regions and hotspots files
      • Guidelines for using target regions and hotspots files
      • View and manage target regions files
      • View and manage hotspots files
      • Modify a BED file
      • Upload a target regions file
      • Upload a hotspots file
      • BED file formats and examples
        • Target regions BED 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 Ion AmpliSeq Designer custom designs
        • Hotspots file format
          • 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
          • Score and strand fields in uploaded hotspot BED files
        • RNA fusions BED file formats and examples
          • Track line
          • Example BED file entries
    • Test fragments
      • View test fragment details
      • Add a custom test fragment
      • Edit or delete a custom test fragment
    • Barcodes and barcode sets
      • View a DNA barcode sequence
      • Download a DNA barcode set CSV file
      • Add a custom DNA barcode set
        • DNA barcode set CSV file setup
      • Delete a custom DNA barcode set
    • Upload history
  • Data management
    • View disk usage parameters
    • View category statistics
    • View active data management jobs
      • Error messages
      • Disk full message
    • Search for run reports with disk usage status
    • Keep run report data
    • Import data for data transfers or restoration
    • View the data management actions log
  • Supported software modules
    • Analysis pipeline overview
    • BaseCaller module and barcode classification overview
      • Overview of the BaseCaller module functionality
        • Notes about barcode classification and barcode filtering
      • Ion Torrent BAM format
      • Custom BAM recorder tags
      • BaseCaller module arguments
        • About BaseCaller module parameters
        • Barcode classification parameters
          • Cutoff setting
          • Separation setting
        • Other public parameters
      • About barcodes
      • Troubleshooting barcode classification issues
        • Explanation of fields in the BaseCaller JSON file
          • Barcode bias
          • Barcode distance histogram
          • Barcode errors histogram
          • Barcode match filtered
          • Filtered
          • Read count
    • 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
      • TMAP alignment refinement
  • Administer Torrent Suite Software
    • Open the Site Administration screen
    • Install Torrent Suite Software
      • Manage Torrent Suite Software user accounts
        • Approve or reject a new user account
        • Modify a user account
        • Delete a single user account
        • Delete multiple user accounts
        • Create a new administrator account to change a password
      • Add customer support contacts
      • Change the time zone for the Ion Torrent Server
      • Change the displayed server name
      • Lock current Torrent Suite Software version
    • Update Torrent Suite Software
      • Update Torrent Suite Software
      • Check for off-cycle updates
      • Enable off-cycle product updates
      • Install off-cycle bundles without Internet access
    • Install or upgrade plugins
      • Enable an installed plugin
      • Configure plugins globally
      • Update off-cycle release plugins
      • Uninstall a plugin
    • Manage disk usage
      • View disk usage parameters
      • Ion instrument data types
      • Archive or delete data automatically
      • Manually export run data
      • Manually archive run data
      • Manually delete selected data from a run report
      • Increase file storage and available disk space
        • Connect to a Torrent Storage NAS (Network Attached Server) device
          • Connect directly to a Torrent Storage NAS (Network Attached Server) device
          • Connect over a network to a Torrent Storage NAS (Network Attached Server) device
          • Monitor the Torrent Storage NAS (Network Attached Server) device
        • USB drives
          • Mount a USB drive
          • Unmount a USB drive
      • Dataflow file sizes
        • Dataflow using the 200-bp kit on the Ion GeneStudio S5 Plus System, Ion GeneStudio S5 Prime System, and Ion S5 XL System
        • Dataflow using the 400-bp kit on the Ion GeneStudio S5 Plus System, Ion GeneStudio S5 Prime System, and Ion S5 XL System
        • Dataflow using the 400-bp kit on the Ion PGM Sequencer
        • Dataflow using the 200-bp kit on the Ion PGM Sequencer and Ion Proton Sequencer
    • Set up flexible workflows
      • View sequencing runs on multiple sequencers with Ion Mesh
      • Transfer a Planned Run to a Ion Torrent Server with Ion Mesh
      • Track Ion Chef Instrument flexible workflows for Ion 550 chips with Ion Mesh
    • Data backup and restore locations
      • Restore the PostgreSQL Database
    • Manage telemetry services
      • Axeda Remote System Monitoring (RSM)
        • Remote access for troubleshooting
        • Axeda RSM agent overview
        • Port assignments
      • Deep Laser
      • Data automatically collected by the telemetry services
        • Ion Torrent Server data
        • Ion PGM data
        • Ion S5, Ion Proton, and Ion GeneStudio S5 System data
    • Administration with command-line utilities
      • Monitor disk space
      • Change the hostname
      • Change the time zone
      • Add an HTTP proxy
      • Alternate checks
  • Screen descriptions
    • User and account settings screen
    • Analysis Parameters screen
    • Configure screen
    • Ion Reporter configuration screen
    • Plugins screen
    • Updates screen
    • References Sequences screen
    • Services screen
    • Planned Runs screen
    • Samples screen
    • Templates screen
    • Runs in Progress screen
    • Ion Chef screen
    • Completed Runs & Reports screen
    • Run Report screen
    • Projects screen
    • Data Management screen
  • Troubleshooting
    • Troubleshooting resources
    • Troubleshoot Torrent Suite Software
      • Get technical support files for a completed run
      • Troubleshoot a sequencing run
      • Customer Support Archive (CSA)
        • Generate a customer support archive
        • Customer support archive contents
      • Troubleshoot IonReporterUploader plugin account setup
      • Troubleshooting file import/upload errors
    • Troubleshoot Ion Torrent Server
      • Check crawler and job server status
        • Queue status
      • Verify network connectivity and name resolution
      • Verify the Ion Torrent Server IP address
      • Troubleshoot and configure the time service
      • Verify file transfer
      • View system support diagnostics
      • View instrument diagnostics
      • Restart services
      • Further investigation and problem resolution
  • Documentation and support
    • Customer and technical support
    • Limited product warranty
  • Legal

Index

Glossary

  • 50Q10 Reads
  • 50Q17 Reads
  • adapter dimer (ISPs)
  • aligned reads
  • BAM file
  • barcode
  • base calling
  • basecalling input file
  • bead loading
  • BED file
  • bp
  • cellularity (%)
  • clonal ISP
  • CNV
  • control sequence
  • CSV file
  • custom template
  • DAT file
  • de novo assembly
  • empty wells
  • enrichment (%)
  • FASTA file
  • FASTQ file
  • FD (flow disruptiveness)
  • flow order
  • fusions
  • hotspots file
  • IA
  • INDEL
  • intermediate files
  • Ion Mesh
  • Ion Torrent Server API
  • ISPs
  • key signal
  • library ISPs
  • library key
  • LIMS metadata
  • live ISP
  • low quality ISP
  • mapped reads
  • mean raw accuracy
  • MNP
  • on target reads
  • output files
  • Planned Run
  • Planned Run template
  • polyclonal ISP
  • preinstalled Planned Run template
  • primer dimer ISP
  • proband
  • Q score
  • Q10
  • Q17
  • Q17 bases
  • Q20
  • Q20 bases
  • read
  • read length
  • reference library
  • relationship group
  • SAM file
  • sample
  • signal processing input files
  • SNP
  • structural variants
  • system SNR
  • target base coverage
  • target regions file
  • test fragment
  • test fragment ISPs
  • test fragment key
  • TF key peak counts
  • total reads
  • TSV file
  • uBAM file
  • unaligned reads
  • uniformity of base coverage
  • usable sequence / usable reads
  • VCF file
  • wells with ISPs
  • XLS file
  • aligned read length
  • AQ score
  • average base coverage depth
  • average base read depth
  • final library reads
  • flow
  • flow transfer

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Ion Reporter™ configuration screen

How to…

Learn more about…

Set up an account for IonReporterUploader plugin

IonReporterUploader plugin configuration

Automatically transfer Torrent Suite Software output to Ion Reporter Software

IonReporterUploader plugin file transfer progress

Manage the Ion Reporter Software analysis workflow list

Ion Reporter™ account setup troubleshooting in Troubleshoot IonReporterUploader plugin account setup

View IonReporterUploader plugin status details

Torrent Suite Software output and Ion Reporter Software analysis phases

Tune IonReporterUploader plugin speed parameters

Related Topics
Parent topic: Screen descriptions

For Research Use Only. Not for use in diagnostic procedures.

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