# 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 |