TruSeq Small RNA v1.0

PreviousTruSeq RNA Exome v1.0 NextTruSeq Stranded mRNA v2.0

Last updated 1 month ago

Overview

TruSeq Small RNA v1.0 includes the following functionality:

Preconfigured TruSeq Small RNA v1.0 protocol that explains how to prepare total RNA or purified small RNA using a Illumina® TruSeq® Small RNA Library Prep Kit.
Automated calculation of sample and buffer volumes.
Automated calculation or display of reagents at every step in the protocol.
Automatic step transition when required.
Automatic placement of samples when necessary.
Automated assignment of QC Pass/Fail, based on user-selected threshold values.
A routing script that allows sequencing of libraries using any Illumina sequencing instrument.

It is not required to have the total RNA samples quantified prior to starting this protocol, however it is highly recommended to ensure the starting number of samples.

Protocol 1: TruSeq Small RNA v1.0

Protocol Type = Library Prep

Next Steps Configuration

Step 1: Ligate Adapters (TruSeq Small RNA v1.0)

Master Step Name = Ligate Adapters (TruSeq Small RNA v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- T4 RNA Ligase 2, Deletion Mutant
  - Supplier = Epicentre
  - Catalog Number = LR2D1132K; LR2D11310K
- TruSeq Small RNA Library Prep Kit, Core Solutions
  - Supplier = Illumina
  - Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html
- TruSeq Small RNA Library Prep Kit, Indices A, B, C or D
  - Supplier = Illumina
  - Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html
Control Types
- Human Brain Total RNA
  - Supplier = Thermo Fisher Scientific
  - Catalog Number = AM7962

Automations

Calculate Master Mix

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/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} &&  /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 '(step.::HML Volume (ul):: = step.::Total samples:: * 2.2) ; (step.::RNase Inhibitor Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::T4 RNA Ligase 2, Depletion Mutant Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::RA5 Volume (ul):: = step.::Total samples:: * 1.21) ; (step.::10mM ATP Volume (ul):: = step.::Total samples:: * 1.21) ; (step.::T4 RNA Ligase Volume (ul):: = step.::Total samples:: * 1.21)' -log {compoundOutputFileLuid1}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 2: Perform Reverse Transcription (TruSeq Small RNA v1.0)

Master Step Name = Perform Reverse Transcription (TruSeq Small RNA v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- SuperScript II Reverse Transcriptase
  - Supplier = Life Technologies
  - Catalog Number = 18064-014
  - Website = http://www.lifetechnologies.com/order/catalog/product/18064014
- TruSeq Small RNA Library Prep Kit, Core Solutions
  - Supplier = Illumina
  - Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html
- TruSeq Small RNA Library Prep Kit, Indices A, B, C or D
  - Supplier = Illumina
  - Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

Automations

Calculate Master Mix

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/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} && /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 '(step.::5X First Strand Buffer Volume (ul):: = step.::Total samples:: * 2.2) ; (step.::12.5 mM dNTP Mix Volume (ul):: = step.::Total samples:: * 0.55) ; (step.::100mM DTT Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::RNase Inhibitor Volume (ul):: = step.::Total samples:: * 1.1) ; (step.::SuperScript II Reverse Transcriptase Volume (ul):: = step.::Total samples:: * 1.1)' -log {compoundOutputFileLuid1}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 3: Amplify Libraries (TruSeq Small RNA v1.0)

Master Step Name = Amplify Libraries (TruSeq Small RNA v1.0.10)
Step Type = Add Labels
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq Small RNA Library Prep Kit, Core Solutions
  - Supplier = Illumina
  - Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html
- TruSeq Small RNA Library Prep Kit, Indices A, B, C or D
  - Supplier = Illumina
  - Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

Automations

Calculate Master Mix

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/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} && /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 '(step.::Ultrapure water Volume (ul):: = step.::Total samples:: * 9.35) ; (step.::PML Volume (ul):: = step.::Total samples:: * 27.5) ; (step.::RP1 Volume (ul):: = (step.::Total samples:: * 2.2).round(2)) ' -log {compoundOutputFileLuid1}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- Tube

Add Labels

Label Groups
- TruSeq Small RNA

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Log File - Automatically attached
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

Step 4: Bioanalyzer QC (Library Validation) (TruSeq Small RNA v1.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input 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 script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -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 script:addBlankLines -i {stepURI:v2} -u {username} -p {password} -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 -i {processURI:v2} -u {username} -p {password} 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 - Output PASS/FAIL

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7} && /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 'output.::Concentration:: = output.::Region 1 Conc.:: ; input.::Concentration:: = output.::Concentration:: ; output.::Conc. Units:: = ::ng/ul:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid8}"

Parse Bioanalyzer XML, Calculate nM and assign QC flags

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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 'output.::Concentration:: = output.::Region 1 Conc.:: ; output.::Molarity (nM):: = (output.::Concentration:: * 1000000) / (660 * output.::Region 1 Average Size - bp::) ; input.::Molarity (nM):: = output.::Molarity (nM):: ; output.::Conc. Units:: = ::ng/ul::' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Parse Bioanalyzer XML, Copy nM and Assign QC flags

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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 'if (output.::Conc. Units::.contains(::pg::)) {output.::Molarity (nM):: = output.::Region 1 Molarity:: / 1000} else {output.::Molarity (nM):: = output.::Region 1 Molarity::} ; (input.::Molarity (nM):: = output.::Molarity (nM)::) ' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- BioAnalyzer DNA High Sensitivity Chip
- BioAnalyzer DNA 1000 Chip

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Bioanalyzer Input File - Automatically attached
- Bioanalyzer Input 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 = Column
- File Column Options
  - File Column Display = Hide
  - File Attachment Method = Auto
- Table Columns - Global Fields

Step 5: Run Gel Electrophoresis and Recover Purified Construct (TruSeq Small RNA v1.0)

Master Step Name = Run Gel Electrophoresis and Recover Purified Construct (TruSeq Small RNA v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- Novex TBE gels, 6%, 10 well
  - Supplier = Life Technologies
  - Catalog Number = EC6265BOX
- Novex TBE running buffer (5X)
  - Supplier = Invitrogen
  - Catalog Number = LC6675
- TruSeq Small RNA Library Prep Kit, Core Solutions
  - Supplier = Illumina
  - Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Gel Image - Manually uploaded
Sample Table
- Sample Display Default = Collapse
- Well Sort Order = Row
- Table Columns - Global Fields

Step 6: Concentrate Final Library (TruSeq Small RNA v1.0)

Master Step Name = Concentrate Final Library (TruSeq Small RNA v1.0.10)
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {SubmittedSampleName}
Reagent Kits
- TruSeq Small RNA Library Prep Kit, Core Solutions
  - Supplier = Illumina
  - Catalog Number = RS-200-0012; RS-200-0024; RS-200-0036; RS-200-0048
  - Website = https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-small-rna.html

Automations

Calculate Master Mix for Pellet Paint

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 '(step.::Total samples:: = step.::Total samples:: + 1)' -log {compoundOutputFileLuid0} && /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 'if (step.::Is Pellet Paint being used?:: == ::Yes:: ) {(step.::Optional - Ultrapure water Volume (ul):: = step.::Total samples:: * 1.98) ; (step.::Optional - 1X Pellet Paint NF Co-Precipitant Volume (ul):: = step.::Total samples:: * 0.22) ; (step.::0.1X Pellet Paint Volume (ul):: = 2)}'  -log {compoundOutputFileLuid1}"

Set Next Step - Advance

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table
- Column Headers
- Expanded View Fields

Record Details

Step Data (Master Step Fields)
Step File Placeholders
- Log File - Automatically attached
- Log File - Automatically attached
Sample Table
- Sample Display Default = Expand
- Well Sort Order = Row
- Table Columns - Global Fields

Step 7: Bioanalyzer QC (Library Validation) (TruSeq Small RNA v1.0)

Master Step Name = Bioanalyzer QC (Library Validation) v2.0
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName} Bioanalyzer

Automations

Generate Bioanalyzer Input 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 script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -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 script:addBlankLines -i {stepURI:v2} -u {username} -p {password} -f {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1} -sep COMMA -b ',False,' -h 1 -c LIMSID -pre 'Sample '"

Parse Bioanalyzer XML, Calculate nM 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 -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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 'output.::Concentration:: = output.::Region 1 Conc.:: ; output.::Molarity (nM):: = (output.::Concentration:: * 1000000) / (660 * output.::Region 1 Average Size - bp::) ; input.::Molarity (nM):: = output.::Molarity (nM):: ; output.::Conc. Units:: = ::ng/ul::' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Set Next Step - Output PASS/FAIL

Trigger Location = Record Details
Trigger Style = Automatic upon exit

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}"

Parse Bioanalyzer XML and assign QC flags

Trigger Location = Not Used

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

Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7} && /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 'output.::Concentration:: = output.::Region 1 Conc.:: ; input.::Concentration:: = output.::Concentration:: ; output.::Conc. Units:: = ::ng/ul:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid8}"

Parse Bioanalyzer XML, Copy nM and Assign QC flags

Trigger Location = Not Used

bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:parseBioAnalyzer -inputFile {compoundOutputFileLuid2} -log {compoundOutputFileLuid5} -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' && /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 'if (output.::Conc. Units::.contains(::pg::)) {output.::Molarity (nM):: = output.::Region 1 Molarity:: / 1000} else {output.::Molarity (nM):: = output.::Region 1 Molarity::} ; (input.::Molarity (nM):: = output.::Molarity (nM)::) ' -log {compoundOutputFileLuid8} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {processURI:v2} -u {username} -p {password} script:assignQC -log {compoundOutputFileLuid6} -qcResult {compoundOutputFileLuid7}"

Queue/Ice Bucket

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Row
Sample Table (Column Headers)

Placement = Enabled

Defaults
- Sample Grouping = Group by Containers
- Well Sort Order = Column
- Placement Pattern = Column
Destination Containers
- BioAnalyzer DNA High Sensitivity Chip
- BioAnalyzer DNA 1000 Chip

Record Details

Group of Defaults

Nextera DNA Flex Library Validation

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 = 1,500.00

Nextera Mate Pair Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 400.00

Nextera XT DNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00

NRCC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 350.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 1,000.00

TruSeq ChIP-Seq Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 400.00

TruSeq Exome Library Validation

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

TruSeq Methyl Capture EPIC Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 300.00

TruSeq Rapid Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 500.00

TruSeq RNA Access Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 320.00

TruSeq RNA Exome Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Peak 2 Size - bp
Criteria 1 - Threshold Value = 200.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Peak 2 Size - bp
Criteria 2 - Threshold Value = 320.00

TruSeq Small RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 100.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 200.00

TruSeq Stranded mRNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00

TruSeq Stranded Total RNA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 250.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Average Size - bp
Criteria 2 - Threshold Value = 275.00

TruSeq Targeted RNA Expression Library Validation

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

TruSight Myeloid Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 150.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00

TruSight RNA Fusion Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 160.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 700.00

TSCA Library Validation

Criteria 1 - Operator = >=
Criteria 1 - Source Data Field = Region 1 Average Size - bp
Criteria 1 - Threshold Value = 300.00
Criteria 2 - Operator = <=
Criteria 2 - Source Data Field = Region 1 Size - bp
Criteria 2 - Threshold Value = 400.00

Step Data
- Group of Defaults = TruSeq Small RNA Library Validation
- Master Step Fields