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GenomeStudio v1.0

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Overview

The GenomeStudio workflow includes the following functionality.

  • Automatic Generation of a sample sheet for genotyping or methylation. These sample sheets can then be used in GenomeStudio to create a project.

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Protocol 1: Infinium Genotyping Analysis (GenomeStudio v1.0)

Protocol Type = Sample Analysis

Next Steps Configuration

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Step 1: Create Infinium Genotyping Analysis Sample Sheet (GenomeStudio v1.0)

  • Master Step Name = Create Infinium Genotyping Analysis Sample Sheet - GenomeStudio v1.0

  • Step Type = No Outputs

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Automations

chevron-rightGenerate GenomeStudio Genotyping Sample Sheethashtag
  • Trigger Location = Record Details

  • Trigger Style = Manual button

chevron-rightSet Next Step - Advancehashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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Queue

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

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Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

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Record Details

  • Step Data (Master Step Fields)

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Protocol 2: Infinium Methylation Analysis (GenomeStudio v1.0)

Protocol Type = Data Analysis

Next Steps Configuration

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Step 1: Create Infinium Methylation Analysis Sample Sheet (GenomeStudio v1.0)

  • Master Step Name = Create Infinium Methylation Analysis Sample Sheet - GenomeStudio v1.0

  • Step Type = No Outputs

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Automations

chevron-rightGenerate GenomeStudio Methylation Sample Sheethashtag
  • Trigger Location = Record Details

  • Trigger Style = Manual button

chevron-rightSet Next Step - Advancehashtag
  • Trigger Location = Record Details

  • Trigger Style = Automatic upon exit

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Queue/Ice Bucket

  • Defaults

    • Sample Grouping = Group by Containers

    • Well Sort Order = Row

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Record Details

  • Step Data (Master Step Fields)

Sample Table (Column Headers)

Category

Field Name

Field Type

Options

Additional Options and Dropdown Items

Container

Container Name

Built-in

Container

Well

Built-in

Sample Table (Column Headers)

Category

Field Name

Field Type

Options

Additional Options and Dropdown Items

Container

Container Name

Built-in

Container

LIMS ID (Container)

Built-in

  • Step File Placeholders

    • GenomeStudio Genotyping Sample Sheet - Automatically attached

    • File Generation Log - Automatically attached

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • Well Sort Order = Row

    • Table Columns - Global Fields

  • Sample Table (Column Headers)

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    Well

    Built-in

    Step File Placeholders
    • GenomeStudio Methylation Sample Sheet - Automatically attached

    • File Generation Log - Automatically attached

    • Log - Automatically attached

  • Sample Table

    • Sample Display Default = Collapse

    • Well Sort Order = Row

    • Table Columns - Global Fields

  • Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    BeadPool Manifest

    Text

    Required Field

    Comment

    Multiline Text

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Comment

    Multiline Text

    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/driverfiletemplates/genomeStudio_Genotyping_SampleSheet_driver_file.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
          script:evaluateDynamicExpression \
          -t false \
          -h false \
          -exp 'nextStep = ::ADVANCE::' \
          -log {compoundOutputFileLuid0}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/driverfiletemplates/genomeStudio_Methylation_SampleSheet_driver_file.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}"
    bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
          script:evaluateDynamicExpression \
          -t false \
          -h false \
          -exp 'nextStep = ::ADVANCE::' \
          -log {compoundOutputFileLuid0}"

    BeadChip Position

    Text

    Read Only

    Derived Sample

    DNA Plate Barcode

    Text

    Read Only

    Derived Sample

    Infinium Kit Name

    Text

    Read Only

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Sample_Well

    Text

    Project

    Project Name

    Built-in

    Well

    Built-in

    Derived Sample

    Array Secondary Analysis

    Text Dropdown

    • Presets

      • GS-GENOTYPING

      • GS-METHYLATION

    Derived Sample

    BeadChip Barcode

    Text

    Read Only

    Derived Sample

    BeadChip Position

    Text

    Read Only

    Derived Sample

    DNA Plate Barcode

    Text

    Read Only

    Derived Sample

    Infinium Kit Name

    Text

    Read Only

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Sample_Well

    Text

    Project

    Project Name

    Built-in

    Derived Sample

    Infinium Kit Name

    Text

    Read Only

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

    Container

    Well

    Built-in

    Derived Sample

    Infinium Kit Name

    Text

    Read Only

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Derived Sample

    Array Secondary Analysis

    Text Dropdown

    • Presets

      • GS-GENOTYPING

      • GS-METHYLATION

    • Default = GS-GENOTYPING

    Derived Sample

    BeadChip Barcode

    Text

    Read Only

    Derived Sample

    Infinium Kit Name

    Text

    Read Only

    Derived Sample

    Sample Name

    Built-in

    Derived Sample

    Waiting

    Built-in

    Project

    Project Name

    Built-in

    Category

    Field Name

    Field Type

    Options

    Additional Options and Dropdown Items

    Container

    Container Name

    Built-in

    Container

    LIMS ID (Container)

    Built-in

    Derived Sample

    Container

    Default = GS-GENOTYPING