DNA Initial QC 5.1.2

Overview

The initial DNA QC protocol contains steps to track quality control data from commonly used QC instruments. Through data integrations, QC data can be added to Clarity LIMS directly from the instrument outputs.

Highlights of this protocol include:

• Data integrations for Bioanalyzer 2100, Nanodrop 8000, CaliperGX, and Tapestation 2200, including creation of the input file and parsing of data output.

• Assignment of pass/fail QC based on chosen criteria.

• Aggregation of data from multiple QC steps.

Protocol 1: DNA Initial QC 5.1.2

• Protocol Type = QC

• Capacity = 100

• QC Filters

  • Bioanalyzer QC (DNA) 5.1.2

    • Did not pass - Bioanalyzer QC (DNA) 5.1.2

  • NanoDrop QC (DNA) 5.1.2

    • Did not pass - NanoDrop QC (DNA) 5.1.2

  • Qubit QC (DNA) 5.1.2

    • Did not pass - Qubit QC (DNA) 5.1.2

  • PicoGreen QC (DNA) 5.1.2

    • Did not pass - PicoGreen QC (DNA) 5.1.2

  • CaliperGX QC 5.1.2

    • Did not pass - CaliperGX QC 5.1.2

  • Tapestation QC (DNA) 5.1.2

    • Did not pass - Tapestation QC (DNA) 5.1.2

  • Aggregate QC (DNA) 5.1.2

    • Passed - Bioanalyzer QC (DNA) 5.1.2 OR

    • Passed - NanoDrop QC (DNA) 5.1.2 OR

    • Passed - Qubit QC (DNA) 5.1.2 OR

    • Passed - PicoGreen QC (DNA) 5.1.2 OR

    • Passed - CaliperGX QC 5.1.2 OR

    • Passed - Tapestation QC (DNA) 5.1.2

Step: Bioanalyzer QC (DNA) 5.1.2

• Master Step Name = Bioanalyzer QC (DNA) 5.1.2

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer driver file

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -u {username} -p {password} \
      script:driver_file_generator \
        -i {processURI:v2} \
        -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv \
        -o {compoundOutputFileLuid0}.csv \
        -l {compoundOutputFileLuid1}  \
      && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \
      script:addBlankLines \
        -i {stepURI:v2} \
        -f {compoundOutputFileLuid0}.csv \
        -l {compoundOutputFileLuid1} \
        -sep COMMA \
        -b ',False,' \
        -h 1 \
        -c LIMSID \
        -pre 'Sample '"

Parse Bioanalyzer XML and assign QC flags

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {processURI:v2} \
      script:parseBioAnalyzer \
        -inputFile {compoundOutputFileLuid2} \
        -log {compoundOutputFileLuid5} \
        -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' \
      script:assignQC \
        -log {compoundOutputFileLuid6} \
        -qcResult {compoundOutputFileLuid7}"

Set Next Step - Advance

• Trigger Location = Record Details

• Trigger Style = Manual button

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 true \
      -h false \
      -exp 'nextStep = ::ADVANCE::' \
      -log {compoundOutputFileLuid0}"

Set Next Step - Output PASS/FAIL

• Trigger Location = Record Details

• Trigger Style = Manual button

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 true -h false -excludeControls true -exp 'if (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}"

Set Next Step and Copy to Input

• Trigger Location = Record Details

• Trigger Style = Manual button

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 true -h false -exp 'nextStep = ::ADVANCE:: ; input.::Concentration (ng/ul):: = output.::Concentration::' -log {compoundOutputFileLuid7}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Projects

  • Well Sort Order = Row

• Sample Table

  • Column Headers

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in
    Submitted Sample	Sample Type	Text

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Workflow	Text
    Project	Project Name	Built-in

Placement = Enabled

• Defaults

  • Sample Grouping = Group by Projects

  • Well Sort Order = Row

  • Placement Pattern = Column

• Destination Containers

  • BioAnalyzer DNA High Sensitivity Chip

  • BioAnalyzer DNA 1000 Chip

Record Details

Group of Defaults

NRCC

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 150.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 1,000.00

• Use strict matching for Bioanalyzer results = No

Peak 2 Size Thresholds

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 100.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 1,000.00

• Use strict matching for Bioanalyzer results = No

TruSeq ChIP-Seq

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Region 1 Molarity

• Criteria 1 - Threshold Value = 5.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Region 1 Molarity

• Criteria 2 - Threshold Value = 10.00

• Use strict matching for Bioanalyzer results = No

TruSeq Methyl Capture EPIC

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 100.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 300.00

TruSeq Rapid Exome

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = Peak 2 Size - bp

• Criteria 1 - Threshold Value = 150.00

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = Peak 2 Size - bp

• Criteria 2 - Threshold Value = 1,000.00

• Use strict matching for Bioanalyzer results = No

• Step Data

  • Step Data Heading = Begin by uploading the required Bioanalyzer XML result file

  • Group of Defaults = Peak 2 Size Thresholds

  • Master Step Fields

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Criteria 1 - Operator	Text Dropdown		Presets >= <= = !=
    Criteria 1 - Source Data Field	Text Dropdown		Presets Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
    Criteria 1 - Threshold Value	Numeric		Decimal Places Displayed = 2
    Criteria 2 - Operator	Text Dropdown		Presets >= <= = !=
    Criteria 2 - Source Data Field	Text Dropdown		Presets Concentration Conc. Units Number of Peaks found Peak 1 Size - bp Peak 1 Conc. Peak 1 Molarity Peak 2 Size - bp Peak 2 Conc. Peak 2 Molarity Peak 3 Size - bp Peak 3 Conc. Peak 3 Molarity Peak 4 Size - bp Peak 4 Conc. Peak 4 Molarity Peak 5 Size - bp Peak 5 Conc. Peak 5 Molarity Number of Regions found Region 1 Average Size - bp Region 1 Conc. Region 1 Molarity Region 2 Average Size - bp Region 2 Conc. Region 2 Molarity Region 3 Average Size - bp Region 3 Conc. Region 3 Molarity Region 4 Average Size - bp Region 4 Conc. Region 4 Molarity Region 5 Average Size - bp Region 5 Conc. Region 5 Molarity
    Criteria 2 - Threshold Value	Numeric		Decimal Places Displayed = 2
    Use strict matching for Bioanalyzer results	Toggle Switch		Default = None Set

• Step File Placeholders

  • Bioanalyzer Driver File - Automatically attached

  • Bioanalyzer Driver File Generation Log File - Automatically attached

  • Bioanalyzer XML Result File (required) - Manually uploaded

  • Result File (optional) - Manually uploaded

  • PDF Summary File (optional) - Manually uploaded

  • Bioanalyzer XML Parsing Log File - Automatically attached

  • QC Assignment Log File - Automatically attached

  • QC Assignment Report - Automatically attached

• Sample Table

  • Enable QC Flags = Yes

  • Sample Display Default = Expand

  • Well Sort Order = Row

  • File Column Options

    • File Column Display = Hide

    • File Attachment Method = Auto

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Measurement	BA Sample Name	Text
    Measurement	Concentration	Numeric		Decimal Places Displayed = 2
    Measurement	Conc. Units	Text
    Measurement	Number of Peaks found	Numeric		Decimal Places Displayed = 0
    Measurement	Number of Regions found	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 1 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 1 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 1 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 2 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 2 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 2 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 3 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 3 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 3 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 4 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 4 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 4 Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Peak 5 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 5 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Peak 5 Size - bp	Numeric		Decimal Places Displayed = 2
    Measurement	Region 1 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 1 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 1 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 2 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 2 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 2 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 3 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 3 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 3 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 4 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 4 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 4 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Region 5 Average Size - bp	Numeric		Decimal Places Displayed = 0
    Measurement	Region 5 Conc.	Numeric		Decimal Places Displayed = 2
    Measurement	Region 5 Molarity	Numeric		Decimal Places Displayed = 2
    Measurement	Sample Comment	Text
    Project	Project Name	Built-in

Step: NanoDrop QC (DNA) 5.1.2

• Master Step Name = NanoDrop QC (DNA) 5.1.2

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName} NanoDrop

Automations

Generate NanoDrop driver file

• Trigger Location = Record Details

• Trigger Style = Automatic upon entry

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -u {username} -p {password} \
      script:driver_file_generator \
        -i {processURI:v2} \
        -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/nd_driver_file_template.csv \
        -o {compoundOutputFileLuid0}.csv \
        -l {compoundOutputFileLuid1}"

Parse NanoDrop NDT and assign QC flags

• Trigger Location = Record Details

• Trigger Style = Manual button

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {processURI:v2} \
      script:parseCSV \
        -inputFile {compoundOutputFileLuid2} \
        -log {compoundOutputFileLuid3} \
        -headerRow '2' \
        -separator 'TAB' \
        -sampleLocation 'Sample ID' \
        -measurementUDFMap 'Concentration::ng/ul' \
        -measurementUDFMap 'A260/280 ratio::260/280' \
        -measurementUDFMap 'A260/230 ratio::260/230' \
        -measurementUDFMap 'A260::260' \
        -relaxed 'true' \
      script:assignQC \
        -log {compoundOutputFileLuid4} \
        -qcResult {compoundOutputFileLuid5}"

Queue/Ice Bucket

• Defaults

  • Sample Grouping = Group by Projects

  • Well Sort Order = Row

• Sample Table

  • Column Headers

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Derived Sample	Waiting	Built-in
    Submitted Sample	Sample Type	Text

  • Expanded View Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Derived Sample	Workflow	Text
    Project	Project Name	Built-in

Record Details

Group of Defaults

A260/A280 Thresholds

• Criteria 1 - Operator = >=

• Criteria 1 - Source Data Field = A260/280 ratio

• Criteria 1 - Threshold Value = 1.70

• Criteria 2 - Operator = <=

• Criteria 2 - Source Data Field = A260/280 ratio

• Criteria 2 - Threshold Value = 2.00

• Step Data

  • Step Data Heading = Begin by uploading the required NanoDrop NDT result file

  • Group of Defaults = A260/A280 Thresholds

  • Master Step Fields

    Field Name	Field Type	Options	Additional Options and Dropdown Items
    Criteria 1 - Operator	Text Dropdown		Presets >= <= = != Default = >=
    Criteria 1 - Source Data Field	Text Dropdown		Presets A260/280 ratio Concentration A260 A260/230 ratio Default = A260/280 ratio
    Criteria 1 - Threshold Value	Numeric		Default = 1.7 Decimal Places Displayed = 2
    Criteria 2 - Operator	Text Dropdown		Presets <= >= = != Default = <=
    Criteria 2 - Source Data Field	Text Dropdown		Presets A260/280 ratio Concentration A260 A260/230 ratio Default = A260/280 ratio
    Criteria 2 - Threshold Value	Numeric		Default = 2.0 Decimal Places Displayed = 2

• Step File Placeholders

  • NanoDrop Driver File - Automatically attached

  • NanoDrop Driver File Generation Log File - Automatically attached

  • NanoDrop NDT Result File (required) - Manually uploaded

  • NanoDrop NDT Parsing Log File - Automatically attached

  • QC Assignment Log File - Automatically attached

  • QC Assignment Report - Automatically attached

• Sample Table

  • Enable QC Flags = Yes

  • Sample Display Default = Collapse

  • Well Sort Order = Row

  • File Column Options

    • File Column Display = Hide

    • File Attachment Method = Auto

  • Table Columns - Global Fields

    Category	Field Name	Field Type	Options	Additional Options and Dropdown Items
    Container	Container Name	Built-in
    Container	Well	Built-in
    Derived Sample	Sample Name	Built-in
    Measurement	A260	Numeric		Decimal Places Displayed = 2
    Measurement	A260/230 ratio	Numeric		Decimal Places Displayed = 2
    Measurement	A260/280 ratio	Numeric		Decimal Places Displayed = 2
    Measurement	Concentration	Numeric		Decimal Places Displayed = 2
    Measurement	Conc. Units	Text
    Project	Project Name	Built-in

Step: Qubit QC (DNA) 5.1.2

• Master Step Name = Qubit QC (DNA) 5.1.2

• Step Type = Standard QC

• Measurement Generation = Fixed, 1

• Naming Convention = {InputItemName} Qubit

Automations

Assign QC flags

• Trigger Location = Record Details