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