TruSeq RNA Access
Overview
The TruSeq RNA Access v1.0 workflow includes the following functionality:
| • | Preconfigured TruSeq RNA Access v1.0 protocol that supports the conversion of total RNA or FFPE samples into a library of template molecules suitable for subsequent cluster generation and sequencing. |
| • | Automated calculation of sample and buffer volumes. |
| • | Automated calculation or display of reagents at every step in the workflow. |
| • | Automatic step transition when required. |
| • | Automatic placement of samples when necessary. |
| • | Automated generation of Bioanalyzer input file that the user may upload to the Bioanalyzer instrument’s Expert Software and use to set up a run. |
| • | Automated parsing of a Bioanalyzer instrument's XML result file into the LIMS, and storing of QC measurement records for the completed run. |
| • | Automated assignment of QC Pass/Fail, based on user-selected threshold values. |
| • | Routing script that allows sequencing of libraries using any Illumina sequencing instrument. |
Protocol 1: TruSeq RNA Access v1.0
Step 1: Sort Samples v.10
Master Step 1: Sort Samples v1.0
Process Type 1: Sort Samples v1.0
Note: As this protocol can be used for FFPE and total RNA samples, and the FFPE samples do not need Fragmentation, this sort step is used to bypass the Fragmentation step.
Input = RNA Samples
Output = no output
Record Details =
| • | Step UDF |
| • | Multi-line text: Comment |
Next Step = either Fragment RNA or First Strand cDNA Synthesis
Step 2: Fragment RNA (TruSeq RNA Access v1.0)
Master Step 2: Fragment RNA v1.0
Process Type 2: Fragment RNA (TruSeq RNA Access v1.0)
Input = 10ng Total RNA or > 20ng Degraded RNA
Output = DFP Plate
SharedResultFile = Log File
Reagent Kits =
| • | TruSeq RNA Access - 12 Index Set A or B, Box 2 - for EPH and RSB |
| – | Set A Part # 15052311 |
| – | Set B Part # 15052312 |
Record Details =
| • | Step UDF |
| • | Multi-line text: Comment |
| – | Single-line Text: |
| – | Thermal Cycler Program Preset: Elution 2 - Frag - Prime |
| • | AnalyteNumeric: Derived Sample - Buffer Volume (ul) - calculated |
| – | Numeric: Derived Sample - Sample Volume (ul) - calculated |
| • | Script description |
| • | Dilute Total RNA |
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 ' output.::Sample Volume (ul):: = 10 / input.::Concentration:: ; output.::Buffer Volume (ul):: = 8.5 - output.::Sample Volume (ul):: ' -log {compoundOutputFileLuid0}["]
Next Step = Set Next Step - Advance
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}["]
Automatic Transition to Next Step
Step 3: First Strand cDNA Synthesis (TruSeq RNA Access v1.0)
Master Step 3: First Strand cDNA Synthesis v1.0
Process Type 3: First Strand cDNA Synthesis (TruSeq RNA Access v1.0)
Input = DFP Plate
Output = No output
SharedResultFile = Log File
Reagent Kits =
| • | TruSeq RNA Access - cDNA Synthesis-PCR, Box 1 - for FSAPart # 15052309 |
Record Details =
| • | Step UDF |
| • | Multi-line text: Comment |
| – | Single-line Text: |
Thermal Cycler Program Preset: Sythesize 1st Strand
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
Automatic Transition to Next Step
Step 4: Second Strand cDNA Synthesis (TruSeq RNA Access v1.0)
Master Step 4: Second Strand cDNA Synthesis v1.0
Process Type 4: Second Strand cDNA Synthesis (TruSeq RNA Access v1.0)
Input = DFP Plate
Output = ALP Plate
SharedResultFile = Log File
Place Samples = Add Automatic Sample Placement (for 4.x ONLY)
bash -l -c ["]/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/customextensions/96_to_96 -log {compoundOutputFileLuid0}["]
Reagent Kits =
| • | TruSeq RNA Access - cDNA Synthesis-PCR, Box 1 - for SMMPart # 15052309 |
| • | TruSeq RNA Access - 12 Index Set A or B, Box 2 - for RSB |
| – | Set A Part # 15052311 |
| – | Set B Part # 15052312 |
| • | AMPure XP beads |
Record Details =
| • | Step UDFMulti-line text: Comment |
| – | Date: 80% EtOH Prep Date |
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
SAFE Stopping Point - No automatic transition
Step 5: Adenylate 3' Ends (TruSeq RNA Access v1.0)
Master Step 5: Adenylate 3' Ends v1.0
Process Type 5: Adenylate 3' Ends (TruSeq RNA Access v1.0)
Input = ALP Plate
Output = No output
SharedResultFile = Log File
Reagent Kits =
| • | TruSeq RNA Access - 12 Index Set A or B, Box 2 - for RSB and ATL |
| – | Set A Part # 15052311 |
| – | Set B Part # 15052312 |
Record Details =
| • | Step UDF |
| • | Multi-line text: Comment |
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
Automatic Transition to Next Step
Step 6: Ligate Adapters (TruSeq RNA Access v1.0)
Master Step 6: Ligate Adapters v1.0
Process Type 6: Ligate Adapters (TruSeq RNA Access v1.0)
Input = ALP Plate
Output = PCR Plate
SharedResultFile = Log File
Place Samples = Add Automatic Sample Placement (for 4.x ONLY)
bash -l -c ["]/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/customextensions/96_to_96 -log {compoundOutputFileLuid0}["]
Index Lists (4.x) =
| • | TruSeq RNA Access.xml |
Index Lists (5.x) =
| • | TruSeq RNA Access.xlsx |
Reagent Kits =
| • | TruSeq RNA Access - 12 Index Set A or B, Box 2 - for RNA Adapter Indexes, LIG, RSB, and STL |
| – | Set A Part # 15052311 |
| – | Set B Part # 15052312 |
| • | AMPure XP beads |
Record Details =
| • | Step UDFMulti-line text: Comment |
| – | Date: 80% EtOH Prep Date |
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
SAFE Stopping Point - No automatic transition
Step 7: First PCR Amplification (TruSeq RNA Access v1.0)
Master Step 7: Amplification v1.0
Process Type 7: First PCR Amplification (TruSeq RNA Access v1.0)
Input = PCR Plate
Output = TSP1 Plate
Place Samples = Add Automatic Sample Placement (For 4.x ONLY)
bash -l -c ["]/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/customextensions/96_to_96 -log {compoundOutputFileLuid0}["]
Reagent Kits =
| • | TruSeq RNA Access - cDNA Synthesis-PCR, Box 1 - for PMM and PPCPart # 15052309 |
| • | TruSeq RNA Access - 12 Index Set A or B, Box 2 - for RSB |
| – | Set A Part # 15052311 |
| – | Set B Part # 15052312 |
| • | AMPure XP beads |
Record Details =
| • | Step UDFMulti-line text: Comment |
| – | Date: 80% EtOH Prep Date |
| – | Single-line Text: |
Thermal Cycler Program Preset: PCR
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
SAFE Stopping Point - No automatic transition
Step 8: Bioanalyzer QC (Library Validation) 5.0
Master Step 8: Bioanalyzer QC (Library Validation) v1.0
Process Type 8: Bioanalyzer QC (Library Validation) 5.0
Input = TSP1 Plate
Output = Result File
Record Details =
| • | Step UDF Criteria 1 - Source Data Field Preset: Peak 2 Size - bp |
| – | Criteria 1 - Operator Preset: >= |
| – | Criteria 1 - Threshold Preset: 200 |
| – | Criteria 2 - Source Data Field Preset: Peak 2 Size - bp |
| – | Criteria 2 - Operator Preset: <= |
| – | Criteria 2 - Threshold Value Preset: 320 |
| – | BA Instrument |
| • | Preset:TruSeq RNA Access Library Validation |
| • | Script descriptionParse Bioanalyzer XML and assign QC flags |
Next Step = Set Next Step - Advance
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}["]
SAFE Stopping Point - No automatic transition
Step 9: First Hybridization (TruSeq RNA Access v1.0)
Master Step 9: Hybridize with Pooling v1.0
Process Type 9: First Hybridization (TruSeq RNA Access v1.0)
Input = TSP1 Plate
Output = RAH1 Plate
SharedResultFile = Log File
Reagent Kits =
| • | TruSeq RNA Access - Coding Transcriptome, Box 4 - for CT3 and CEXPart # 15052314 |
Record Details =
| • | Step UDFMulti-line text: Comment |
| – | Single-line Text: |
Thermal Cycler Program Preset: RNA HYB
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
Automatic Transition to Next Step
Step 10: First Capture (TruSeq RNA Access v1.0)
Master Step 10: Capture Hybridized Probes v1.0
Process Type 10: First Capture (TruSeq RNA Access v1.0)
Input = RAH1 Plate
Output = RAH2 Plate
Place Samples = Add Automatic Sample Placement (For 4.x ONLY)
bash -l -c ["]/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/customextensions/96_to_96 -log {compoundOutputFileLuid0}["]
Reagent Kits =
| • | TruSeq RNA Access - Coding Capture Reagents, Box 3 - for ET2 and SMBPart # 15052313 |
| • | TruSeq RNA Access - Coding Transcriptome, Box 4 - for HP3, EE1 and EWSPart # 15052314 |
Record Details =
| • | Step UDF |
| • | Multi-line text: Comment |
| – | Numeric: |
2N NaOH (ul) Not editable
| – | Numeric: |
Enrichment Elution Buffer (ul) Not editable
| – | Numeric: Total Number of SamplesHidden |
| – | Use first preset value |
| – | Preset = 0 |
| • | Script description |
| • | Calculate Master Mix |
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 Number of Samples:: = step.::Total Number of 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.::Enrichment Elution Buffer 1 (ul):: = 28.5 * step.::Total Number of Samples:: ; step.::2N NaOH (ul):: = 1.5 * step.::Total Number of Samples::' -log {compoundOutputFileLuid0}"
Next Step = Set Next Step - Advance
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}["]
SAFE Stopping Point - No automatic transition
Step 11: Second Hybridization (TruSeq RNA Access v1.0)
Master Step 11: Perform Second Hybridization v1.0
Process Type 11:Second Hybridization (TruSeq RNA Access v1.0
Input = RAH2 Plate
Output = No output
SharedResultFile = Log File
Reagent Kits =
| • | TruSeq RNA Access - Coding Transcriptome, Box 4 - for CT3 and CEXPart # 15052314 |
| • | TruSeq RNA Access - 12 Index Set A or B, Box 2 - for RSB |
| – | Set A Part # 15052311 |
| – | Set B Part # 15052312 |
Record Details =
| • | Step UDF |
| • | Multi-line text: Comment |
| – | Single-line Text: |
Thermal Cycler Program Preset: RNA HYB
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
Automatic Transition to Next Step
Step 12: Second Capture (TruSeq RNA Access v1.0)
Master Step 12: Perform Second Capture v1.0
Process Type 12: Second Capture (TruSeq RNA Access v1.0)
Input = RAH2 Plate
Output = RAC1 Plate
SharedResultFile = Log File
Place Samples = Add Automatic Sample Placement (For 4.x ONLY)
bash -l -c ["]/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/customextensions/96_to_96 -log {compoundOutputFileLuid0}["]
Reagent Kits =
| • | TruSeq RNA Access - Coding Capture Reagents, Box 3 - for ET2 and SMBPart # 15052313 |
| • | TruSeq RNA Access - Coding Transcriptome, Box 4 - for HP3, EE1 and EWSPart # 15052314 |
Record Details =
| • | Step UDFMulti-line text: Comment |
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
Automatic Transition to Next Step
Step 13: Capture Sample Clean Up (TruSeq RNA Access v1.0)
Master Step 13: Clean Up v1.0
Process Type 13:Capture Sample Clean Up (TruSeq RNA Access v1.0)
Input = RAH2 Plate
Output = RAA Plate
SharedResultFile = Log File
Place Samples = Add Automatic Sample Placement (For 4.x ONLY)
bash -l -c ["]/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/ customextensions /96_to_96 -log {compoundOutputFileLuid0}["]
Reagent Kits =
| • | TruSeq RNA Access - 12 Index Set A or B, Box 2 - for RSB |
| – | Set A Part # 15052311 |
| – | Set B Part # 15052312 |
| • | AMPure XP beads |
Record Details =
| • | Step UDF |
| • | Multi-line text: Comment |
| – | Date: 80% EtOH Prep Date |
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
SAFE Stopping Point - No automatic transition
Step 14: Second PCR Amplification (TruSeq RNA Access v1.0)
Master Step 14: Second PCR Amplification v1.0
Process Type 14: Second PCR Amplification (TruSeq RNA Access v1.0)
Input = RAA Plate
Output = no output
SharedResultFile = Log File
Reagent Kits =
| • | TruSeq RNA Access - cDNA Synthesis-PCR, Box 1 - for PPCPart # 15052309 |
| • | TruSeq RNA Access - Coding Transcriptome, Box 4 - for EPMPart # 15052314 |
Record Details =
| • | Step UDFMulti-line text: Comment |
| – | Single-line Text: |
Thermal Cycler Program Preset: EPM AMP
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
SAFE Stopping Point - No automatic transition
Step 15: Second PCR Clean Up (TruSeq RNA Access v1.0)
Master Step 15: Clean Up v1.0
Process Type 15: Second PCR Clean Up (TruSeq RNA Access v1.0)
Input = RAA Plate
Output = RAL Plate
SharedResultFile = Log File
Place Samples = Add Automatic Sample Placement (For 4.x ONLY)
bash -l -c ["]/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/PlacementHelper.jar script:place_samples -i {stepURI:v2} -u {username} -p {password} -d /opt/gls/clarity/extensions/conf/v5/96_to_96 -log {compoundOutputFileLuid0}["]
Reagent Kits =
| • | TruSeq RNA Access - 12 Index Set A or B, Box 2 - for RSB |
| – | Set A Part # 15052311 |
| – | Set B Part # 15052312 |
| • | AMPure XP beads |
Record Details =
| • | Step UDFMulti-line text: Comment |
| – | Date: 80% EtOH Prep Date |
| • | Script description |
Next Step = Set Next Step - Advance
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}["]
Step 16: Bioanalyzer QC (Library Validation) 5.0
Master Step 16: Bioanalyzer QC (Library Validation) v1.0
Process Type 16:Bioanalyzer QC (Library Validation) 5.0
Input = DNA Libraries
Output = Result File
SharedResultFile =
Record Details =
| • | Step UDF |
| – | Criteria 1 - Source Data FieldPreset: Region 1 Average Size - bp |
| – | Criteria 1 - OperatorPreset: >= |
| – | Criteria 1 - ThresholdPreset: 250 |
| – | Criteria 2 - Source Data FieldPreset: Region 1 Average Size - bp |
| – | Criteria 2 - OperatorPreset: <= |
| – | Criteria 2 - Threshold ValuePreset: 275 |
| • | Preset:TruSeq Stranded mRNA Library Validation |
| • | Analyte UDFSample Measurement - Concentration |
| – | Sample Measurement - Conc. Units |
| – | Sample Measurement - Molarity (nM) |
| – | Sample Measurement - Region 1 Average Size - bp |
| – | Sample Measurement - Region 1 Conc. |
| – | Sample Measurement - Region 1 Molarity |
| • | Script description |
| • | Parse Bioanalyzer XML, Calculate nM and assign QC flags |
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}["]
Next Step = Set Next Step - Advance
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}["]
Safe Stopping Point - No transition
Step 17: Normalize Libraries (TruSeq RNA Access v1.0)
Master Step 17: Normalize Libraries 1 v1.0
Process Type 17: Normalize Libraries (TruSeq RNA Access v1.0)
Input = Purified cDNA construct Tube
Output = Normalized libraries Tube
Record Details =
| • | Step UDF |
| – | Multi-line Text: Comment |
| – | Numeric: Target Normalization (nM) |
| – | Preset: 2 |
| – | Mandatory |
| – | Numeric: Final Volume (ul)Mandatory |
| • | Analyte UDFNumeric: Derived Sample - Molarity (nM) - copied in from input |
| – | Numeric: Derived Sample - Sample Volume (ul) - copied down from step UDF Sample Volume (ul) |
| – | Numeric: Derived Sample - Buffer Volume (ul) - calculated in the EPP trigger |
| – | Numeric: Normalized Molarity (nM) Mandatory |
| – | Single-line Text: Sequencing Instrument |
Mandatory
| – | Presets =MiSeq |
| – | NextSeq |
| – | HiSeq2500 |
| – | HiSeq3000/4000 |
| – | NovaSeq |
| – | HiSeqX |
| • | Script description Normalization Calculations - Option 1 |
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 'output.::Molarity (nM):: = input.::Molarity (nM):: ; if (output.::Molarity (nM):: <= step.::Target Normalization (nM)::) {output.::Sample Volume (ul):: = step.::Final Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = (step.::Target Normalization (nM):: * step.::Final Volume (ul):: ) / input.::Molarity (nM):: ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul):: ; output.::Normalized Molarity (nM):: = step.::Target Normalization (nM)::}' -log {compoundOutputFileLuid0}["]Next Step = Set Next Step script to REMOVE
Next Step = Set Next Step - Remove
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 = ::REMOVE::' -log {compoundOutputFileLuid0} ["]
Finish Step = Routing script - Normalize Libraries
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 {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\ --FIELD_NAME ' Sequencing Instrument ' \--FIELD_VALUE 'MiSeq' \--WORKFLOW 'MiSeq Sequencing v1.0' \--STEP 'Library Pooling (MiSeq v1.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS' \\--FIELD_NAME ' Sequencing Instrument ' \--FIELD_VALUE 'NextSeq' \--WORKFLOW 'NextSeq 500/550 Sequencing v1.0' \--STEP 'Library Pooling (NextSeq 500/550 v1.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS' \\--FIELD_NAME ' Sequencing Instrument ' \--FIELD_VALUE 'HiSeq2500' \--WORKFLOW 'HiSeq 2500 Sequencing v1.0' \--STEP 'Library Pooling (HiSeq 2500 v1.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS' \\--FIELD_NAME ' Sequencing Instrument ' \--FIELD_VALUE 'HiSeq3000/4000' \--WORKFLOW 'HiSeq 3000/4000 Sequencing v1.0' \--STEP 'Library Pooling (HiSeq 3000/4000 v1.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS' \\--FIELD_NAME ' Sequencing Instrument ' \--FIELD_VALUE 'HiSeqX' \--WORKFLOW 'HiSeq X Sequencing v1.0' \--STEP 'Library Pooling (HiSeq X v1.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS' \\--FIELD_NAME ' Sequencing Instrument ' \--FIELD_VALUE 'NovaSeq' \--WORKFLOW 'NovaSeq 5000/6000 v2.0' \--STEP 'Define Run Format (NovaSeq 5000/6000 v2.0)' \--INPUTS_OR_OUTPUTS 'OUTPUTS'["]
