> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-methyl-capture-epic-v2.0.md). # TruSeq Methyl Capture EPIC v2.0 ## Protocol 1: TruSeq Methyl Capture EPIC v2.0 Protocol Type = Library Prep **Next Steps Configuration**
### Step 1: Fragment DNA (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Fragment DNA (TruSeq Methyl Capture EPIC v2.0) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * Control Types * HCC1187 breast cancer tumor (TruSeq Methyl EPIC v1.0) * Supplier = ATCC * Catalog Number = CRL2322 * HCC1187 normal (BL) (TruSeq Methyl EPIC v1.0) * Supplier = ATCC * Catalog Number = CRL2322-D * Conc. = 20 * Jurkat (TruSeq Methyl EPIC v1.0) * Supplier = Biochain * Catalog Number = D1255815 * NA12878 (TruSeq Methyl EPIC v1.0) * Supplier = Coriell Institute * Catalog Number = NA12878 #### 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} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp '(step.::Total Samples:: = step.::Total Samples:: + 1)' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'step.::RSB (mL):: = step.::Total Samples:: * 5 * 1.1 ; step.::0.5 M EDTA (uL):: = step.::Total Samples:: * 10 * 1.1 ; if (!input.name.contains(::TruSeq Methyl EPIC v1.0::)) {output.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units::}' -log {compoundOutputFileLuid1}" ``` {% endcode %}
Normalize gDNA * 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 'if (input.name.contains( ::(TruSeq Methyl EPIC v1.0)::) ) { output.::Concentration:: = step.::Control Concentration (ng/ul):: ; output.::Conc. Units:: = ::ng/uL:: ; output.::Sample Volume (ul):: = 500 / step.::Control Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = 50 - output.::Sample Volume (ul):: } else {output.::Sample Volume (ul):: = 500 / input.::Concentration:: ; output.::Buffer Volume (ul):: = 50 - output.::Sample Volume (ul)::}' -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 | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Row * Destination Containers * 1x8 Strip Tube
#### Record Details * Step Data (Master Step Fields) | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ----------------------------- | -------------- | -------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Comment | Multiline Text | | | | Control Concentration (ng/ul) | Numeric | Required Field | | | Control Type | Text Dropdown | Custom Entries |

Presets

| | Cycles/Burst | Numeric | | | | Duration (seconds) | Numeric | | | | Duty Factor (%) | Numeric | | | | Peak/Displayed Power (W) | Numeric | | | | RSB (mL) | Numeric | | | | Temperature (C) | Numeric | | | | Total Samples | Numeric | | | | Water Level | Numeric | | | | 0.5 EDTA (uL) | Numeric | | | * Step File Placeholders * Log File - Manually uploaded * 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 | Numeric | 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: Bioanalyzer QC (DNA) (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Bioanalyzer QC (DNA) 5.1.2 * Step Type = Standard QC * Measurement Generation = Fixed, 1 * Naming Convention = {InputItemName} Bioanalyzer #### Automations
Generate Bioanalyzer driver file * Trigger Location = Record Details * Trigger Style = Automatic upon entry {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/DriverFileGenerator.jar -u {username} -p {password} \ script:driver_file_generator \ -i {processURI:v2} \ -t /opt/gls/clarity/extensions/ngs-common/v5/EPP/conf/readonly/bioA_driver_file_template.csv \ -o {compoundOutputFileLuid0}.csv \ -l {compoundOutputFileLuid1} \ && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} \ script:addBlankLines \ -i {stepURI:v2} \ -f {compoundOutputFileLuid0}.csv \ -l {compoundOutputFileLuid1} \ -sep COMMA \ -b ',False,' \ -h 1 \ -c LIMSID \ -pre 'Sample '" ``` {% 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 -u {username} -p {password} -i {processURI:v2} \ script:parseBioAnalyzer \ -inputFile {compoundOutputFileLuid2} \ -log {compoundOutputFileLuid5} \ -configFile '/opt/gls/clarity/extensions/conf/v5/bioanalyzer/defaultBioAnalyzerDNAConfig.groovy' \ script:assignQC \ -log {compoundOutputFileLuid6} \ -qcResult {compoundOutputFileLuid7}" ``` {% 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 true \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Output PASS/FAIL * 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 true -h false -excludeControls true -exp 'if (output.QC == true) { nextStep = ::ADVANCE:: } else { nextStep = ::ESCALATE:: }' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step and 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 true -h false -exp 'nextStep = ::ADVANCE:: ; input.::Concentration (ng/ul):: = output.::Concentration::' -log {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 | 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 | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Column * Destination Containers * BioAnalyzer DNA 1000 Chip
#### Record Details **Group of Defaults**
NRCC * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 150.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 1,000.00 * Use strict matching for Bioanalyzer results = No
Peak 2 Size Thresholds * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 100.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 1,000.00 * Use strict matching for Bioanalyzer results = No
TruSeq ChIP-Seq * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Region 1 Molarity * Criteria 1 - Threshold Value = 5.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Region 1 Molarity * Criteria 2 - Threshold Value = 10.00 * Use strict matching for Bioanalyzer results = No
TruSeq Methyl Capture EPIC * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 100.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 300.00
TruSeq Rapid Exome * Criteria 1 - Operator = >= * Criteria 1 - Source Data Field = Peak 2 Size - bp * Criteria 1 - Threshold Value = 150.00 * Criteria 2 - Operator = <= * Criteria 2 - Source Data Field = Peak 2 Size - bp * Criteria 2 - Threshold Value = 1,000.00 * Use strict matching for Bioanalyzer results = No
* Step Data * Group of Defaults = TruSeq Methyl Capture EPIC * Master Step Fields | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | ------------------------------------------- | -------------- | ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Criteria 1 - Operator | Text Dropdown | |

Presets

| | Criteria 1 - Source Data Field | Text Dropdown | |

Presets

| | Criteria 1 - Threshold Value | Numeric | | Decimal Places Displayed = 2 | | Criteria 2 - Operator | Text Dropdown | |

Presets

| | Criteria 2 - Source Data Field | Text Dropdown | |

Presets

| | Criteria 2 - Threshold Value | Numeric | | Decimal Places Displayed = 2 | | Use strict matching for Bioanalyzer results | Toggle Switch | | Default = None Set | * Step File Placeholders * Bioanalyzer Driver File - Automatically attached * Bioanalyzer Driver 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 = Row * 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** | | -------------- | -------------------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | LIMS ID (Container) | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Measurement | A260/280 ratio | Numeric | | Decimal Places Displayed = 2 | | Measurement | BA Sample Name | Text | | | | Measurement | Concentration | Numeric | | Decimal Places Displayed = 2 | | Measurement | Conc. Units | Text | | | | 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 | | Measurement | Sample Comment | Text | | | | Project | Project Name | Built-in | | | ### Step 3: Clean Up Fragmented DNA (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Clean Up Fragmented DNA (TruSeq Methyl Capture EPIC v2.0) * Step Type = No Outputs * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 4: Repair Ends (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Repair Ends (TruSeq Methyl Capture EPIC v2.0) * Step Type = No Outputs * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 = ERP | | 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 5: Adenylate 3' Ends (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Adenylate 3' Ends v2.0 * Step Type = No Outputs * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 = ATAIL70 | * 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 6: Ligate Adapters (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Ligate Adapters v2.0 * Step Type = Add Labels * Derived Sample Generation = Fixed, 1 * Naming Convention = {SubmittedSampleName} #### 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 and 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 true -h false -exp 'nextStep = ::ADVANCE:: ; input.::Concentration (ng/ul):: = output.::Concentration::' -log {compoundOutputFileLuid7}" ``` {% 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 | | | #### Add Labels * Label Groups * TruSeq Methyl Capture EPIC #### 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 = LIG | | 80% EtOH Prep Date | Date | | | * Step File Placeholders * Log File - Automatically attached * Sample Table * Sample Display Default = Collapse * 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 | Reagent Name | Built-in | | | | Derived Sample | Sample Name | Built-in | | | | Project | Project Name | Built-in | | | ### Step 7: Clean Up and Pool Ligated Fragments (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Clean Up and Pool v2.0 * Step Type = Pooling * Aliquot Generation = Fixed, 1 * Naming Convention = {PoolName} * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 #### Record Details * Step File Placeholders * Log File - Manually uploaded * 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 8: Hybridize Probes (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Hybridize v2.0 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 5 - Probes * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 %}
Library Dilution * 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:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'output.::Library Volume (ul):: = 200 / input.::Concentration (ng/ul):: ; output.::RSB Volume (ul):: = 10 - output.::Library Volume (ul)::' -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 | | | #### Placement = Enabled * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Placement Pattern = Row * Destination Containers * 1x8 Strip Tube
#### 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 = MC HYB1 | | 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 9: Capture Hybridized Probes (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Capture Hybridized Probes v2.0 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 %}
Calculate Master Mix * 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: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 %}
#### 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 10: Perform Second Hybridization (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Perform Second Hybridization v2.0 * Step Type = No Outputs * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 5 - Probes * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 11: Perform Second Capture (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Perform Second Capture (TruSeq Methyl Capture EPIC v2.0) * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### Automations
Set Next Step - IF/ELSE * 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 'if (step.::Bisulfite Conversion?:: == ::True:: ) {nextStep = ::Bisulfite Conversion (TruSeq Methyl Capture EPIC v2.0.11):: } else {nextStep = ::Amplify Enriched Library (TruSeq Methyl Capture EPIC v2.0.11):: }' -log {compoundOutputFileLuid0}" ``` {% endcode %} > ℹ The actual TruSeq Methyl Capture EPIC version used in the automation script may vary depending on the version of IPP installed.
#### 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** | | --------------------- | -------------- | -------------- | -------------------------------------------------- | | Bisulfite Conversion? | Text Dropdown | Required Field |

Presets

  • True
  • False
| | Comment | Multiline Text | | | * Step File Placeholders * Log File - Manually uploaded * 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: Bisulfite Conversion (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Bisulfite Conversion v1.0 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 1 - Bisulphite Conversion Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 Placement Information * 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.::Sample_Plate:: = output.container.name' -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 13: Amplify Enriched Library (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Amplify Enriched Library v2.0 * Step Type = No Outputs * Reagent Kits * KAPA HiFi HotStart Uracil+ Ready Mix (2X) * Supplier = Kapa * Catalog Number = KK2801 * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 14: Clean Up Amplified Enriched Library (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Clean Up v2.0 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} * Reagent Kits * TruSeq Methyl Capture EPIC HT/LT - Box 2 - SPB Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = * TruSeq Methyl Capture EPIC HT/LT - Box 4 - Core Reagents * Supplier = Illumina * Catalog Number = LT Catalog # - FC-151-1002; HT Catalog # - FC-151-1003 * Website = #### 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 15: Bioanalyzer QC (Library Validation) (TruSeq Methyl Capture EPIC v2.0) * 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 = 500.00
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 Methyl Capture EPIC 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 16: Normalize Libraries (TruSeq Methyl Capture EPIC v2.0) * Master Step Name = Normalize Libraries 1 v2.0.10 * Step Type = Standard * Derived Sample Generation = Fixed, 1 * Naming Convention = {InputItemName} {% hint style="info" %} The version of Normalized Libraries 1 master step name may be different depending on the version of IPP installed. {% endhint %} #### Automations
Normalization Calculations - Option 1 * 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.::Molarity (nM):: = input.::Molarity (nM):: ; if (output.::Molarity (nM):: <= step.::Target Normalization (nM)::) {output.::Sample Volume (ul):: = step.::Final Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = (step.::Target Normalization (nM):: * step.::Final Volume (ul):: ) / input.::Molarity (nM):: ; output.::Buffer Volume (ul):: = step.::Final Volume (ul):: - output.::Sample Volume (ul):: ; output.::Normalized Molarity (nM):: = step.::Target Normalization (nM)::}' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Set Next Step - Remove * 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 = ::REMOVE::' -log {compoundOutputFileLuid0}" ``` {% endcode %}
Routing script - Normalize Libraries * Trigger Location = Step * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'MiSeq' \ --WORKFLOW 'MiSeq Sequencing v3.2' \ --STEP 'Library Pooling (MiSeq v3.2)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NextSeq' \ --WORKFLOW 'NextSeq 500/550 Sequencing v1.2' \ --STEP 'Library Pooling (NextSeq 500/550 v1.2)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NovaSeq 2.0' \ --WORKFLOW 'NovaSeq 6000 v2.3' \ --STEP 'Define Run Format (NovaSeq 6000 v2.3)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NovaSeq 3.0' \ --WORKFLOW 'NovaSeq 6000 v3.8' \ --STEP 'Define Run Format (NovaSeq 6000 v3.8)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NovaSeqDx' \ --WORKFLOW 'NovaSeqDx v1.2' \ --STEP 'Define Run Format (NovaSeqDx v1.2)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NextSeq 1000/2000' \ --WORKFLOW 'NextSeq 1000/2000 Sequencing v2.4' \ --STEP 'Library Pooling and Dilution (NextSeq 1000/2000 Sequencing v2.4)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NovaSeq X Series' \ --WORKFLOW 'NovaSeq X Series v1.1' \ --STEP 'Assign Analysis Configuration Template (NovaSeq X Series Sequencing v1.1)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS' \ \ --FIELD_NAME 'Sequencing Instrument' \ --FIELD_VALUE 'NextSeq 1000/2000 On-Prem' \ --WORKFLOW 'NextSeq 1000/2000 On-Prem Sequencing v1.0' \ --STEP 'Library Pooling and Dilution (NextSeq 1000/2000 On-Prem Sequencing v1.0)' \ --INPUTS_OR_OUTPUTS 'OUTPUTS'" ``` {% endcode %} > ℹ The field value and the actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.
#### 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 | | | | Final Volume (ul) | Numeric | Required Field |
  • Decimal Places Displayed = 2
| | Target Normalization (nM) | Numeric | Required Field |
  • Default = 2
  • 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 | Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Buffer Volume (ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Normalized Molarity (nM) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample Volume (ul) | Numeric | | Decimal Places Displayed = 2 | | Derived Sample | Sequencing Instrument | Text Dropdown | Required Field |

Presets

  • MiSeq
  • NextSeq
  • NextSeq 1000/2000
  • NextSeq 1000/2000 On-Prem
  • NovaSeq 2.0
  • NovaSeq 3.0
  • NovaSeq X Series
  • NovaSeqDx
| | Project | Project Name | Built-in | | | > ℹ The preset options for Derived Sample Sequencing Instrument may vary depending on the version of the IPP. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## 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, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/clarity-lims/library-prep/truseq/truseq-methyl-capture-epic-v2.0.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. 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.