# TruSeq RNA Exome v1.0
## Overview
TruSeq RNA Exome v1.0 includes the following functionality:
* Preconfigured TruSeq RNA Exome v1.0 protocol that explains how to convert total RNA into a library of template molecules of known strand origin, then capture the coding regions of the transcriptome using the reagents provided in Illumina® TruSeq® RNA Access Library Prep kits. The resulting library is 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 protocol.
* Automatic step transition when required.
* Automatic placement of samples when necessary.
* Automated assignment of QC Pass/Fail, based on user-selected threshold values.
## Protocol 1: TruSeq RNA Exome v1.0
Protocol Type = Library Prep
**Next Steps Configuration**
### Step 1: Fragment RNA (TruSeq RNA Exome v1.0)
* Master Step Name = Fragment RNA v2.0
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* TruSeq RNA Library Prep for Enrichment
* Supplier = Illumina
* Catalog Number = 20020189
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Dilute Total RNA
* Trigger Location = Record Details
* Trigger Style = Manual button
{% code overflow="wrap" %}
```markup
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):: = (step.::Desired Diluted Concentration (ng/uL):: * 8.5) / input.::Concentration:: ; output.::Buffer Volume (ul):: = 8.5 - output.::Sample Volume (ul):: ; output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------------- | -------------- | -------------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| Desired Diluted Concentration (ng/uL) | Numeric | Required Field | Decimal Places Displayed = 1 |
| Thermal Cycler Program | Text | | Default = Elution 2 - Frag - Prime |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | -------------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Buffer Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Concentration | Numeric | Required Field | Decimal Places Displayed = 2 |
| Derived Sample | Conc. Units | Text | Required Field | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 |
| Project | Project Name | Built-in | | |
### Step 2: Synthesize First Strand cDNA (TruSeq RNA Exome v1.0)
* Master Step Name = First Strand cDNA Synthesis v2.0
* Step Type = No Outputs
* Reagent Kits
* SuperScript II Reverse Transcriptase
* Supplier = Life Technologies
* Catalog Number = 18064-014
* Website =
* TruSeq RNA Library Prep for Enrichment
* Supplier = Illumina
* Catalog Number = 20020189
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Column
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------- | -------------- | -------------- | ----------------------------------------------------------------------------------------------------------------------------- |
| Comment | Multiline Text | | |
| Thermal Cycler Program | Text Dropdown | Custom Entries | Presets
- Synthesize 1st Strand
- 1stSS
- Default = Synthesize 1st Strand
|
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 3: Synthesize Second Strand cDNA (TruSeq RNA Exome v1.0)
* Master Step Name = Second Strand cDNA Synthesis v2.0
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* AMPure XP Beads
* Supplier = Beckman Coulter Genomics
* Catalog Number = A63881
* Website =
* TruSeq RNA Library Prep for Enrichment
* Supplier = Illumina
* Catalog Number = 20020189
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------ | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| 80% EtOH Prep Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Column
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 4: Adenylate 3' Ends (TruSeq RNA Exome v1.0)
* Master Step Name = Adenylate 3' Ends v2.0
* Step Type = No Outputs
* Reagent Kits
* TruSeq RNA Library Prep for Enrichment
* Supplier = Illumina
* Catalog Number = 20020189
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------------- | -------------- | ----------- | ----------------------------------------- |
| ATL to add to each well (uL) | Numeric | | Default = 12.5 |
| Comment | Multiline Text | | |
| RSB to add to each well (uL) | Numeric | | Default = 2.5 |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Column
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 5: Ligate Adapters (TruSeq RNA Exome v1.0)
* Master Step Name = Ligate Adapters v2.0
* Step Type = Add Labels
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* AMPure XP Beads
* Supplier = Beckman Coulter Genomics
* Catalog Number = A63881
* Website =
* TruSeq RNA Library Prep for Enrichment
* Supplier = Illumina
* Catalog Number = 20020189
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Copy to Output
* Trigger Location = Not Used
{% code overflow="wrap" %}
```markup
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 'output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
Set Next Step & Copy to Input
* Trigger Location = Not Used
{% code overflow="wrap" %}
```markup
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:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Add Labels
* Label Groups
* TruSeq RNA Single Indexes (12 indexes, 24 samples) Set A
* TruSeq RNA Single Indexes (12 indexes, 24 samples) Set B
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| --------------------------------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| Round 1 EtOH to each well (uL) | Numeric | | Default = 42 |
| Round 1 RSB to each well (uL) | Numeric | | Default = 52.5 |
| Round 2 EtOH to each well (uL) | Numeric | | Default = 50 |
| Round 2 RSB to each well (uL) | Numeric | | Default = 22.5 |
| 1 RSB to add to each well (uL) | Numeric | | Default = 2.5 |
| 2 LIG to add to each well (uL) | Numeric | | Default = 2.5 |
| 3 RNA Adapters to add to each well (uL) | Numeric | | Default = 2.5 |
| 80% EtOH Prep Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Reagent Name | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 6: Enrich DNA Fragments (TruSeq RNA Exome v1.0)
* Master Step Name = Enrich DNA Fragments (TruSeq RNA Exome v1.0.6)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
* AMPure XP Beads
* Supplier = Beckman Coulter Genomics
* Catalog Number = A63881
* Website =
* TruSeq RNA Library Prep Enrichment Component, Box 1
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
* TruSeq RNA Library Prep for Enrichment
* Supplier = Illumina
* Catalog Number = 20020189
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| Thermal Cycler Program | Text | | Default = PCR |
| 80% EtOH Prep Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 7: Bioanalyzer QC (Library Validation) (TruSeq RNA Exome 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
{% code overflow="wrap" %}
```markup
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 '"
```
{% endcode %}
Parse Bioanalyzer XML and assign QC flags
* Trigger Location = Record Details
* Trigger Style = Manual button
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Set Next Step - Output PASS/FAIL
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations
* Trigger Location = Not Used
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Parse Bioanalyzer XML, Calculate nM and assign QC flags
* Trigger Location = Not Used
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Parse Bioanalyzer XML, Copy nM and Assign QC flags
* Trigger Location = Not Used
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### 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 RNA Exome Library Validation
* Master Step Fields
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------------------- | -------------- | -------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Criteria 1 - Operator | Text Dropdown | Custom Entries | 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 | Custom Entries | 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 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
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------------------- | -------------- | ----------- | ----------------------------------------- |
| Derived Sample | Molarity (nM) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Measurement | BA Sample Name | Text | | |
| Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 |
| Measurement | Conc. Units | Text | | |
| Measurement | Molarity (nM) | Numeric | | Decimal Places Displayed = 2 |
| 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 |
### Step 8: Hybridize Probes (TruSeq RNA Exome v1.0)
* Master Step Name = Hybridize with Pooling v2.0
* Step Type = Pooling
* Aliquot Generation = Fixed, 1
* Naming Convention = {PoolName}
* Reagent Kits
* TruSeq RNA Library Prep Coding Exome Oligos
* Supplier = Illumina
* Catalog Number = 20020183
* Website = [www.illumina.com](https://www.illumina.com)
* TruSeq RNA Library Prep Enrichment Component, Box 2
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Pooling
* Label Uniqueness = On
* Defaults
* Sample Grouping = Group by Containers
* Well Sort Order = Row
#### Placement = Enabled
* Defaults
* Well Sort Order = Row
* Placement Pattern = Column
* Destination Containers
* 96 well plate
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------- | -------------- | -------------- | ------------------------------------------------------- |
| Comment | Multiline Text | | |
| Thermal Cycler Program | Text Dropdown | Custom Entries | Presets
|
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 9: Capture Hybridized Probes (TruSeq RNA Exome v1.0)
* Master Step Name = Capture Hybridized Probes v2.0
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* TruSeq RNA Library Prep Enrichment Component, Box 1
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
* TruSeq RNA Library Prep Enrichment Component, Box 2
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Calculate Master Mix
* Trigger Location = Record Details
* Trigger Style = Automatic upon entry
{% code overflow="wrap" %}
```markup
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -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:http} -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}"
```
{% endcode %}
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------------------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| Enrichment Elution Buffer 1 (ul) | Numeric | | Decimal Places Displayed = 2 |
| 2N NaOH (ul) | Numeric | | Decimal Places Displayed = 2 |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 10: Second Hybridization (TruSeq RNA Exome v1.0)
* Master Step Name = Perform Second Hybridization v2.0
* Step Type = No Outputs
* Reagent Kits
* TruSeq RNA Library Prep Coding Exome Oligos
* Supplier = Illumina
* Catalog Number = 20020183
* Website = [www.illumina.com](https://www.illumina.com)
* TruSeq RNA Library Prep Enrichment Component, Box 2
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------------------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| Thermal Cycler Program RNA Exome | Text | | Default = RNA HYB |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 11: Second Capture (TruSeq RNA Exome v1.0)
* Master Step Name = Perform Second Capture v2.0
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* TruSeq RNA Library Prep Enrichment Component, Box 1
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
* TruSeq RNA Library Prep Enrichment Component, Box 2
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 12: Clean Up Captured Library (TruSeq RNA Exome v1.0)
* Master Step Name = Clean Up v2.0
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
* AMPure XP Beads
* Supplier = Beckman Coulter Genomics
* Catalog Number = A63881
* Website =
* TruSeq RNA Library Prep Enrichment Component, Box 2
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------ | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| 80% EtOH Prep Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 13: Amplify Enriched Library (TruSeq RNA Exome v1.0)
* Master Step Name = Second PCR Amplification v1.0
* Step Type = No Outputs
* Reagent Kits
* TruSeq RNA Library Prep Enrichment Component, Box 2
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ---------------------- | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| Thermal Cycler Program | Text | | Default = EPM AMP |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 14: Clean Up Amplified Enriched Library (TruSeq RNA Exome v1.0)
* Master Step Name = Clean Up v2.0
* Step Type = Standard
* Reagent Kits
* AMPure XP Beads
* Supplier = Beckman Coulter Genomics
* Catalog Number = A63881
* Website =
* TruSeq RNA Library Prep Enrichment Component, Box 2
* Supplier = Illumina
* Catalog Number = 20020490
* Website = [www.illumina.com](https://www.illumina.com)
#### Automations
Set Next Step - Advance
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | | |
* Expanded View Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | LIMS ID (Container) | Built-in | | |
| Project | Project Name | Built-in | | |
#### Record Details
* Step Data (Master Step Fields)
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------ | -------------- | ----------- | ----------------------------------------- |
| Comment | Multiline Text | | |
| 80% EtOH Prep Date | Date | | |
* Step File Placeholders
* Log File - Automatically attached
* Sample Table
* Sample Display Default = Expand
* Well Sort Order = Row
* Table Columns - Global Fields
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
| Container | Container Name | Built-in | | |
| Container | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Project | Project Name | Built-in | | |
### Step 15: Bioanalyzer QC (Library Validation) (TruSeq RNA Exome 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
{% code overflow="wrap" %}
```markup
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 '"
```
{% endcode %}
Parse Bioanalyzer XML, Calculate nM and assign QC flags
* Trigger Location = Record Details
* Trigger Style = Manual button
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Set Next Step - Output PASS/FAIL
* Trigger Location = Record Details
* Trigger Style = Automatic upon exit
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Parse Bioanalyzer XML and assign QC flags
* Trigger Location = Not Used
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations
* Trigger Location = Not Used
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
Parse Bioanalyzer XML, Copy nM and Assign QC flags
* Trigger Location = Not Used
{% code overflow="wrap" %}
```markup
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}"
```
{% endcode %}
#### Queue/Ice Bucket
* Defaults
* Sample Grouping = Group by Containers
* 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 | LIMS ID (Container) | Built-in | | |
| Container | Well | Built-in | | |
| Derived Sample | Sample Name | Built-in | | |
| Derived Sample | Waiting | Built-in | | |
| Project | Project Name | Built-in | | |
#### 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 RNA Exome Library Validation
* Master Step Fields
| **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| ------------------------------------------- | -------------- | -------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Criteria 1 - Operator | Text Dropdown | Custom Entries | 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 | Custom Entries | 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 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
| **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
| -------------- | -------------------------- | -------------- | ----------- | ----------------------------------------- |
| Derived Sample | Molarity (nM) | Numeric | | Decimal Places Displayed = 2 |
| Derived Sample | Sample Name | Built-in | | |
| Measurement | BA Sample Name | Text | | |
| Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 |
| Measurement | Conc. Units | Text | | |
| Measurement | Molarity (nM) | Numeric | | Decimal Places Displayed = 2 |
| 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 |
---
# Agent Instructions: Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.
Perform an HTTP GET request on the current page URL with the `ask` query parameter:
```
GET https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-rna-exome-v1.0.md?ask=
```
The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.
Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.