> 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-dna-exome-v2.0.md).

# TruSeq DNA Exome v2.0

## Overview

The TruSeq DNA Exome v2.0 includes the following functionality:

* Preconfigured TruSeq DNA Exome v2.0 protocol that supports the preparation of 96 indexed, paired-end libraries, followed by enrichment using reagents provided in an Illumina® TruSeq® Exome Kit.
* Automated calculation of sample and buffer volumes.
* Automated calculation or display of reagents at every step in the protocol.
* Automatic step transition when required.
* Automatic placement of samples when necessary.
* Automated assignment of QC Pass/Fail, based on user-selected threshold values.
* A routing script that allows sequencing of libraries to any Illumina sequencing instrument.

## Protocol 1: Library Prep (TruSeq DNA Exome v2.0)

Protocol Type = Library Prep

**Next Steps Configuration**

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-b375306d4597d01b567830ef4a8da56d16313f37%2Ftruseq-dna-exome-next-step-config.png?alt=media" alt=""><figcaption></figcaption></figure>

### Step 1: Normalize DNA (TruSeq DNA Exome v2.0)

* Master Step Name = Normalize DNA (TruSeq DNA Exome v2.0.10)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of Normalize DNA master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-358c73382fb968433dcdd03cea55d4bf0e2b6f09%2Ftruseq-dna-exome-step1-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Calculate Sample Volume &#x26; Shearing Buffer Mix</summary>

* 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.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
output.::Sample Volume (uL):: = step.::DNA Amount (ng):: / output.::Concentration:: ; \
output.::Shearing Buffer Mix (uL):: = step.::Total Volume (uL):: - output.::Sample Volume (uL)::' \
-log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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 = 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**                                             |
  | ----------------- | -------------- | ----------- | ------------------------------------------------------------------------------------- |
  | DNA Amount (ng)   | Numeric        | Read Only   | <ul><li>Default = 100</li></ul>                                                       |
  | EDTA (uL)         | Numeric        | Read Only   | <ul><li>Default = 10</li></ul>                                                        |
  | Notes             | Multiline Text | Read Only   | <ul><li>Default = DNA Amout (ng) and Total Volume (uL) are both per sample.</li></ul> |
  | RSB (mL)          | Numeric        | Read Only   | <ul><li>Default = 5</li></ul>                                                         |
  | Total Volume (uL) | Numeric        | Read Only   | <ul><li>Default = 50</li><li>Decimal Places Displayed = 0</li></ul>                   |
* Step File Placeholders
  * Log - 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 | 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              |
    | Derived Sample | Shearing Buffer Mix (uL) | Numeric        |                | Decimal Places Displayed = 0              |
    | Project        | Project Name             | Built-in       |                |                                           |

### Step 2: Fragment DNA (TruSeq DNA Exome v2.0)

* Master Step Name = Fragment DNA (TruSeq Exome v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-74d986a7017a2e19b70044f7bff1e2b342144d7a%2Ftruseq-dna-exome-step2-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

<details>

<summary>Normalize gDNA</summary>

* 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 Volume (ul):: = 100 / input.::Concentration (ng/ul):: ; output.::Buffer Volume (ul):: = 50 - output.::Sample Volume (ul):: ' -log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

#### 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 = Row
  * Placement Pattern = Column
* Destination Containers
  * Tube
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**             | **Field Type**   | **Options**    | **Additional Options and Dropdown Items**                                                                                      |
  | -------------------------- | ---------------- | -------------- | ------------------------------------------------------------------------------------------------------------------------------ |
  | Comment                    | Multiline Text   |                |                                                                                                                                |
  | Covaris Cycles/Burst       | Numeric          |                | <ul><li>Default = 200</li><li>Decimal Places Displayed = 0</li></ul>                                                           |
  | Covaris Duration (seconds) | Numeric Dropdown | Custom Entries | <ul><li><p>Presets</p><ul><li>375</li><li>280</li><li>360</li><li>420</li></ul></li><li>Decimal Places Displayed = 0</li></ul> |
  | Covaris Duty Factor (%)    | Numeric Dropdown | Custom Entries | <ul><li><p>Presets</p><ul><li>20</li><li>10</li><li>30</li></ul></li><li>Decimal Places Displayed = 0</li></ul>                |
  | Covaris Intensifier        | Text Dropdown    | Custom Entries | <ul><li><p>Presets</p><ul><li>Yes</li><li>No</li></ul></li></ul>                                                               |
  | Covaris Intensity          | Numeric          |                | <ul><li>Decimal Places Displayed = 0</li></ul>                                                                                 |
  | Covaris Peak Power (W)     | Numeric Dropdown | Custom Entries | <ul><li><p>Presets</p><ul><li>50</li><li>175</li><li>450</li></ul></li><li>Decimal Places Displayed = 0</li></ul>              |
  | Covaris Temperature (C)    | Numeric Dropdown | Custom Entries | <ul><li><p>Presets</p><ul><li>20</li><li>7</li></ul></li><li>Decimal Places Displayed = 0</li></ul>                            |
  | Covaris Water Level        | Numeric Dropdown | Custom Entries | <ul><li><p>Presets</p><ul><li>12</li><li>6</li></ul></li><li>Decimal Places Displayed = 0</li></ul>                            |
* 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: Clean Up Fragmented DNA (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-49539af84cec2d3255d37150b232bd03fe90206b%2Ftruseq-dna-exome-step3-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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 = Row
  * Placement Pattern = Column
* Destination Containers
  * Tube
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**     | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------ | -------------- | ----------- | ----------------------------------------- |
  | 80% EtOH Prep Date | Date           |             |                                           |
* Step File Placeholders
  * Log - 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 and Select Library Size (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-e9a49bd9599c88933385d85c1e699e1d6c4f9be8%2Ftruseq-dna-exome-step4-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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 = Row
  * Placement Pattern = Column
* Destination Containers
  * Tube
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**         | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ---------------------- | -------------- | ----------- | ----------------------------------------- |
  | Thermal Cycler Program | Text           |             | Default = ERP                             |
  | 80% EtOH Prep Date     | Date           |             |                                           |
* Step File Placeholders
  * Log - 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: Ligate Adapters (TruSeq DNA Exome v2.0)

* Master Step Name = Ligate Adapters (TruSeq DNA Exome v2.0.10)
* Step Type = Add Labels
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}-{AppliedReagentLabels}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of Ligate Adapters master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-8a25764e148831b47606e2f31d8637628bb6e422%2Ftruseq-dna-exome-step5-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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 = Row
  * Placement Pattern = Column
* Destination Containers
  * Tube
  * 96 well plate

#### Add Labels

* Label Groups
  * IDT-ILMN TruSeq DNA-RNA UD 24 Indexes
  * IDT-ILMN TruSeq DNA-RNA UD 24 Indexes Plate
  * IDT-ILMN TruSeq DNA-RNA UD 96 Indexes Plate
  * TruSeq Exome
  * TruSeq Exome HT
  * TruSeq Exome LT

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**         | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ---------------------- | -------------- | ----------- | ----------------------------------------- |
  | Thermal Cycler Program | Text           |             | Default = LIG                             |
  | 80% EtOH Prep Date     | Date           |             |                                           |
* Step File Placeholders
  * Log - 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: Enrich DNA Fragments (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-3dbd47c66b94ab7ee63a5daeb86b0226cda55dbd%2Ftruseq-dna-exome-step6-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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 = Row
  * Placement Pattern = Column
* Destination Containers
  * Tube
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**                  | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------------------- | -------------- | ----------- | ----------------------------------------- |
  | PCR Cycles                      | Numeric        |             |                                           |
  | Thermal Cycler Program - Enrich | Text           |             | Default = PCRNano                         |
  | 80% EtOH Prep Date              | Date           |             |                                           |
* Step File Placeholders
  * Log - 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: Qubit DNA QC (TruSeq DNA Exome v2.0)

* Master Step Name = Qubit DNA QC (TruSeq Exome v1.0)
* Step Type = Standard QC
* Measurement Generation = Fixed, 2
* Naming Convention = {SubmittedSampleName}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-8a8553819ff778b24ca9978e67ce63e5c0ac3862%2Ftruseq-dna-exome-step7-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Average Concentration &#x26; Assign QC flags</summary>

* 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:computeReplicateAverage -src 'Concentration' -dest 'Concentration' -log {compoundOutputFileLuid3} && /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 {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}  && /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 'input.::Concentration:: = output.::Concentration::' -log {compoundOutputFileLuid3}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**                 | **Field Type** | **Options** | **Additional Options and Dropdown Items**                          |
  | ------------------------------ | -------------- | ----------- | ------------------------------------------------------------------ |
  | Criteria 1 - Source Data Field | Text           |             | Default = Concentration                                            |
  | Criteria 1 - Operator          | Text Dropdown  |             | <p>Presets</p><ul><li>>=</li><li><=</li><li>=</li><li>!=</li></ul> |
  | Criteria 1 - Threshold Value   | Numeric        |             | Decimal Places Displayed = 2                                       |
  | Criteria 2 - Source Data Field | Text           |             | Default = Concentration                                            |
  | Criteria 2 - Operator          | Text Dropdown  |             | <p>Presets</p><ul><li>>=</li><li><=</li><li>=</li><li>!=</li></ul> |
  | Criteria 2 - Threshold Value   | Numeric        |             | Decimal Places Displayed = 2                                       |
* Step File Placeholders
  * Qubit Result File - Manually uploaded
  * QC Assignment Log File - Manually uploaded
  * QC Assignment Report File - Manually uploaded
  * Log File - 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 | Concentration       | Numeric        | Required Field | Decimal Places Displayed = 2              |
    | Derived Sample | Conc. Units         | Text           | Required Field |                                           |
    | Derived Sample | Sample Name         | Built-in       |                |                                           |
    | Measurement    | Concentration       | Numeric        |                | Decimal Places Displayed = 2              |
    | Measurement    | Conc. Units         | Text           |                |                                           |
    | Project        | Project Name        | Built-in       |                |                                           |

### Step 8: Bioanalyzer QC (TruSeq DNA Exome v2.0)

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

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-daa8979f8268b39249009849f7b222b840f0c467%2Ftruseq-dna-exome-step8-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Generate Bioanalyzer Input file</summary>

* 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 %}

</details>

<details>

<summary>Parse Bioanalyzer XML and assign QC flags</summary>

* 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 %}

</details>

<details>

<summary>Set Next Step - Output PASS/FAIL</summary>

* 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 %}

</details>

<details>

<summary>Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations</summary>

* 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 %}

</details>

<details>

<summary>Parse Bioanalyzer XML, Calculate nM and assign QC flags</summary>

* 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 %}

</details>

<details>

<summary>Parse Bioanalyzer XML, Copy nM and Assign QC flags</summary>

* 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 %}

</details>

#### 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

  <figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-b01a3d1277eb9352528522ca613f83cae1d7c7c6%2Fbioanalyzer-dna-high-sensitivity-chip-container.png?alt=media" alt=""><figcaption></figcaption></figure>

  * BioAnalyzer DNA 1000 Chip

  <figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-28c00d95372efbcc2c4cb08969972a094491630e%2Fbioanalyzer-dna-1000-chip-container.png?alt=media" alt=""><figcaption></figcaption></figure>

#### Record Details

**Group of Defaults**

<details>

<summary>Nextera DNA Flex Library Validation</summary>

* 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

</details>

<details>

<summary>Nextera Mate Pair Library Validation</summary>

* 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

</details>

<details>

<summary>Nextera XT DNA Library Validation</summary>

* 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

</details>

<details>

<summary>NRCC Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq ChIP-Seq Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Exome Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Methyl Capture EPIC Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Rapid Exome Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq RNA Access Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq RNA Exome Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Small RNA Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Stranded mRNA Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Stranded Total RNA Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Targeted RNA Expression Library Validation</summary>

* 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

</details>

<details>

<summary>TruSight Myeloid Library Validation</summary>

* 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

</details>

<details>

<summary>TruSight RNA Fusion Library Validation</summary>

* 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

</details>

<details>

<summary>TSCA Library Validation</summary>

* 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

</details>

* Step Data
  * Group of Defaults = TruSeq Exome Library Validation
  * Master Step Fields

    | **Field Name**                              | **Field Type** | **Options**    | **Additional Options and Dropdown Items**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
    | ------------------------------------------- | -------------- | -------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
    | Criteria 1 - Operator                       | Text Dropdown  | Custom Entries | <p>Presets</p><ul><li>>=</li><li><=</li><li>=</li><li>!=</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
    | Criteria 1 - Source Data Field              | Text Dropdown  |                | <p>Presets</p><ul><li>Concentration</li><li>Conc. Units</li><li>Number of Peaks found</li><li>Peak 1 Size - bp</li><li>Peak 1 Conc.</li><li>Peak 1 Molarity</li><li>Peak 2 Size - bp</li><li>Peak 2 Conc.</li><li>Peak 2 Molarity</li><li>Peak 3 Size - bp</li><li>Peak 3 Conc.</li><li>Peak 3 Molarity</li><li>Peak 4 Size - bp</li><li>Peak 4 Conc.</li><li>Peak 4 Molarity</li><li>Peak 5 Size - bp</li><li>Peak 5 Conc.</li><li>Peak 5 Molarity</li><li>Number of Regions found</li><li>Region 1 Average Size - bp</li><li>Region 1 Conc.</li><li>Region 1 Molarity</li><li>Region 2 Average Size - bp</li><li>Region 2 Conc.</li><li>Region 2 Molarity</li><li>Region 3 Average Size - bp</li><li>Region 3 Conc.</li><li>Region 3 Molarity</li><li>Region 4 Average Size - bp</li><li>Region 4 Conc.</li><li>Region 4 Molarity</li><li>Region 5 Average Size - bp</li><li>Region 5 Conc.</li><li>Region 5 Molarity</li></ul> |
    | Criteria 1 - Threshold Value                | Numeric        |                | Decimal Places Displayed = 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
    | Criteria 2 - Operator                       | Text Dropdown  | Custom Entries | <p>Presets</p><ul><li>>=</li><li><=</li><li>=</li><li>!=</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
    | Criteria 2 - Source Data Field              | Text Dropdown  |                | <p>Presets</p><ul><li>Concentration</li><li>Conc. Units</li><li>Number of Peaks found</li><li>Peak 1 Size - bp</li><li>Peak 1 Conc.</li><li>Peak 1 Molarity</li><li>Peak 2 Size - bp</li><li>Peak 2 Conc.</li><li>Peak 2 Molarity</li><li>Peak 3 Size - bp</li><li>Peak 3 Conc.</li><li>Peak 3 Molarity</li><li>Peak 4 Size - bp</li><li>Peak 4 Conc.</li><li>Peak 4 Molarity</li><li>Peak 5 Size - bp</li><li>Peak 5 Conc.</li><li>Peak 5 Molarity</li><li>Number of Regions found</li><li>Region 1 Average Size - bp</li><li>Region 1 Conc.</li><li>Region 1 Molarity</li><li>Region 2 Average Size - bp</li><li>Region 2 Conc.</li><li>Region 2 Molarity</li><li>Region 3 Average Size - bp</li><li>Region 3 Conc.</li><li>Region 3 Molarity</li><li>Region 4 Average Size - bp</li><li>Region 4 Conc.</li><li>Region 4 Molarity</li><li>Region 5 Average Size - bp</li><li>Region 5 Conc.</li><li>Region 5 Molarity</li></ul> |
    | 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 9: Hybridize Probes (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-b4ff2b4602a3eee8d42b86c8432f00121ba973a6%2Ftruseq-dna-exome-step9-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**                     | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ---------------------------------- | -------------- | ----------- | ----------------------------------------- |
  | Thermal Cycler Program - Hybridize | Text           |             | Default = TE HYB                          |
* Step File Placeholders
  * Log - 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: Capture Hybridize Probes (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-e3dc3786786277c5b958f257ca6e4f9efcbff6eb%2Ftruseq-dna-exome-step10-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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       |             |                                           |

#### Record Details

* Step File Placeholders
  * Log - 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 Hybridization (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-8a7f859b7e91a0cd33fc8149096843a2e9c53f15%2Ftruseq-dna-exome-step11-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**                     | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ---------------------------------- | -------------- | ----------- | ----------------------------------------- |
  | Thermal Cycler Program - Hybridize | Text           |             | Default = TE HYB                          |
* Step File Placeholders
  * Log - 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: Perform Second Capture (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-203ab2e0dbdcacf5b03610721ff6c0f54092940f%2Ftruseq-dna-exome-step12-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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 = Row
  * Placement Pattern = Column
* Destination Containers
  * 96 well plate

#### Record Details

* Step File Placeholders
  * Log - 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: Clean Up Captured Library (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-c1720caac34ae3fa5d7c070a9fe21b6d4963e598%2Ftruseq-dna-exome-step13-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**     | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------ | -------------- | ----------- | ----------------------------------------- |
  | 80% EtOH Prep Date | Date           |             |                                           |
* Step File Placeholders
  * Log - 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: Amplify Enriched Library (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-5860fa12a189ae69b2d3fb9184b71ab38db2bc8a%2Ftruseq-dna-exome-step14-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**                   | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | -------------------------------- | -------------- | ----------- | ----------------------------------------- |
  | PCR Cycles                       | Numeric        |             |                                           |
  | Thermal Cycler Program - Amplify | Text           |             | Default = AMP8                            |
* Step File Placeholders
  * Log - 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: Clean Up Amplified Enriched Library (TruSeq DNA Exome v2.0)

* Master Step Name = TruSeq DNA Exome v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}
* Reagent Kits
  * TruSeq Exome Kit
    * Supplier = Illumina
    * Catalog Number = 24 - 20020614; 96 - 20020615
    * Website = [www.illumina.com](https://help.connected.illumina.com/clarity-lims/library-prep/truseq/www.illumina.com)

{% hint style="info" %}
The version of TruSeq DNA Exome master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-ba3585ba63f13948e194c9f33912e4619b11f1f0%2Ftruseq-dna-exome-step15-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Set Next Step - Advance</summary>

* 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 %}

</details>

#### 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 = Row
  * Placement Pattern = Row
* Destination Containers
  * Tube
  * 96 well plate

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**     | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------ | -------------- | ----------- | ----------------------------------------- |
  | 80% EtOH Prep Date | Date           |             |                                           |
* Step File Placeholders
  * Log - 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 16: Bioanalyzer QC (TruSeq DNA Exome v2.0)

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

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-0aff3b9874d3ac3c1860a681f5faf5eb80209a56%2Ftruseq-dna-exome-step16-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Generate Bioanalyzer Input file</summary>

* 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 %}

</details>

<details>

<summary>Parse Bioanalyzer XML, Calculate nM and assign QC flags</summary>

* 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 %}

</details>

<details>

<summary>Set Next Step - Output PASS/FAIL</summary>

* 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 %}

</details>

<details>

<summary>Parse Bioanalyzer XML and assign QC flags</summary>

* 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 %}

</details>

<details>

<summary>Parse Bioanalyzer XML, Assign QC flags, and Copy Concentrations</summary>

* 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 %}

</details>

<details>

<summary>Parse Bioanalyzer XML, Copy nM and Assign QC flags</summary>

* 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 %}

</details>

#### 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

  <figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-b01a3d1277eb9352528522ca613f83cae1d7c7c6%2Fbioanalyzer-dna-high-sensitivity-chip-container.png?alt=media" alt=""><figcaption></figcaption></figure>

  * BioAnalyzer DNA 1000 Chip

  <figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-28c00d95372efbcc2c4cb08969972a094491630e%2Fbioanalyzer-dna-1000-chip-container.png?alt=media" alt=""><figcaption></figcaption></figure>

#### Record Details

**Group of Defaults**

<details>

<summary>Nextera DNA Flex Library Validation</summary>

* 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

</details>

<details>

<summary>Nextera Mate Pair Library Validation</summary>

* 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

</details>

<details>

<summary>Nextera XT DNA Library Validation</summary>

* 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

</details>

<details>

<summary>NRCC Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq ChIP-Seq Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Exome Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Methyl Capture EPIC Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Rapid Exome Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq RNA Access Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq RNA Exome Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Small RNA Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Stranded mRNA Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Stranded Total RNA Library Validation</summary>

* 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

</details>

<details>

<summary>TruSeq Targeted RNA Expression Library Validation</summary>

* 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

</details>

<details>

<summary>TruSight Myeloid Library Validation</summary>

* 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

</details>

<details>

<summary>TruSight RNA Fusion Library Validation</summary>

* 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

</details>

<details>

<summary>TSCA Library Validation</summary>

* 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

</details>

* Step Data
  * Group of Defaults = TruSeq Exome Library Validation
  * Master Step Fields

    | **Field Name**                              | **Field Type** | **Options**    | **Additional Options and Dropdown Items**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
    | ------------------------------------------- | -------------- | -------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
    | Criteria 1 - Operator                       | Text Dropdown  | Custom Entries | <p>Presets</p><ul><li>>=</li><li><=</li><li>=</li><li>!=</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
    | Criteria 1 - Source Data Field              | Text Dropdown  |                | <p>Presets</p><ul><li>Concentration</li><li>Conc. Units</li><li>Number of Peaks found</li><li>Peak 1 Size - bp</li><li>Peak 1 Conc.</li><li>Peak 1 Molarity</li><li>Peak 2 Size - bp</li><li>Peak 2 Conc.</li><li>Peak 2 Molarity</li><li>Peak 3 Size - bp</li><li>Peak 3 Conc.</li><li>Peak 3 Molarity</li><li>Peak 4 Size - bp</li><li>Peak 4 Conc.</li><li>Peak 4 Molarity</li><li>Peak 5 Size - bp</li><li>Peak 5 Conc.</li><li>Peak 5 Molarity</li><li>Number of Regions found</li><li>Region 1 Average Size - bp</li><li>Region 1 Conc.</li><li>Region 1 Molarity</li><li>Region 2 Average Size - bp</li><li>Region 2 Conc.</li><li>Region 2 Molarity</li><li>Region 3 Average Size - bp</li><li>Region 3 Conc.</li><li>Region 3 Molarity</li><li>Region 4 Average Size - bp</li><li>Region 4 Conc.</li><li>Region 4 Molarity</li><li>Region 5 Average Size - bp</li><li>Region 5 Conc.</li><li>Region 5 Molarity</li></ul> |
    | Criteria 1 - Threshold Value                | Numeric        |                | Decimal Places Displayed = 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
    | Criteria 2 - Operator                       | Text Dropdown  | Custom Entries | <p>Presets</p><ul><li>>=</li><li><=</li><li>=</li><li>!=</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
    | Criteria 2 - Source Data Field              | Text Dropdown  |                | <p>Presets</p><ul><li>Concentration</li><li>Conc. Units</li><li>Number of Peaks found</li><li>Peak 1 Size - bp</li><li>Peak 1 Conc.</li><li>Peak 1 Molarity</li><li>Peak 2 Size - bp</li><li>Peak 2 Conc.</li><li>Peak 2 Molarity</li><li>Peak 3 Size - bp</li><li>Peak 3 Conc.</li><li>Peak 3 Molarity</li><li>Peak 4 Size - bp</li><li>Peak 4 Conc.</li><li>Peak 4 Molarity</li><li>Peak 5 Size - bp</li><li>Peak 5 Conc.</li><li>Peak 5 Molarity</li><li>Number of Regions found</li><li>Region 1 Average Size - bp</li><li>Region 1 Conc.</li><li>Region 1 Molarity</li><li>Region 2 Average Size - bp</li><li>Region 2 Conc.</li><li>Region 2 Molarity</li><li>Region 3 Average Size - bp</li><li>Region 3 Conc.</li><li>Region 3 Molarity</li><li>Region 4 Average Size - bp</li><li>Region 4 Conc.</li><li>Region 4 Molarity</li><li>Region 5 Average Size - bp</li><li>Region 5 Conc.</li><li>Region 5 Molarity</li></ul> |
    | 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 17: Normalize Libraries (TruSeq DNA Exome 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 Normalize Libraries 1 master step name may be different depending on the version of IPP installed.
{% endhint %}

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-1fe7e45e96b76ca2fd551605432e5a8411920c9e%2Ftruseq-dna-exome-step17-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Normalization Calculations - Option 1</summary>

* 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 %}

</details>

<details>

<summary>Set Next Step - Remove</summary>

* 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 %}

</details>

<details>

<summary>Routing script - Normalize Libraries</summary>

* 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 actual version of the workflows and steps in the routing automation script may be different depending on the version of IPP installed.

</details>

#### 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       |             |                                           |

#### 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 | <ul><li>Decimal Places Displayed = 2</li></ul>                     |
  | Target Normalization (nM) | Numeric        | Required Field | <ul><li>Default = 2</li><li>Decimal Places Displayed = 2</li></ul> |
* 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 | Molarity (nM)            | 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 | <p>Presets</p><ul><li>MiSeq</li><li>NextSeq</li><li>NextSeq 1000/2000</li><li>NextSeq 1000/2000 On-Prem</li><li>NovaSeq 2.0</li><li>NovaSeq 3.0</li><li>NovaSeq X Series</li><li>NovaSeqDx</li></ul> |
    | 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-dna-exome-v2.0.md?ask=<question>&goal=<endgoal>
```

`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.