> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/clarity-lims/library-prep/truseq/truseq-chip-seq-v1.0.md).

# TruSeq ChIP-Seq v1.0

## Protocol 1: TruSeq ChIP-Seq v1.0

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-494bfdcc2d89d8bf7a92a10191fc53a4ecfab6b1%2Ftruseq-chip-next-step-config.png?alt=media" alt=""><figcaption></figcaption></figure>

### Step 1: Normalize DNA (TruSeq ChIP-Seq v1.0)

* Master Step Name = Normalize DNA (TruSeq ChIP-Seq v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* 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-faa32de54feb43196a1981cfd26dffd7b6a3f40a%2Ftruseq-chip-step1-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Normalization Calculations</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.::Sample Volume (ul):: = (((step.::Input Amount (pg/ul):: / 1000) * step.::Final Volume (ul)::) / input.::Concentration::) ; output.::Buffer Volume (ul):: = step.::Final 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      | Well           | Built-in       |             |                                           |
    | Derived Sample | Sample Name    | Built-in       |             |                                           |
    | Derived Sample | Waiting        | Built-in       |             |                                           |
  * Expanded View Fields

    | **Category** | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container    | LIMS ID (Container) | Built-in       |             |                                           |
    | Project      | Project Name        | Built-in       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**       | **Field Type** | **Options**    | **Additional Options and Dropdown Items**                                    |
  | -------------------- | -------------- | -------------- | ---------------------------------------------------------------------------- |
  | Comment              | Multiline Text |                |                                                                              |
  | Final Volume (ul)    | Numeric        | Required Field | <ul><li>Default = 50</li><li>Decimal Places Displayed = 2</li></ul>          |
  | Input Amount (pg/ul) | Numeric        | Required Field | <ul><li>Range From 100 to 200</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 | Buffer Volume (ul)  | Numeric        |             | Decimal Places Displayed = 2              |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Derived Sample | Sample Volume (ul)  | Numeric        |             | Decimal Places Displayed = 2              |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 2: End Repair (TruSeq ChIP-Seq v1.0)

* Master Step Name = Repair Ends v1.0
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
  * AMPure XP Beads
    * Supplier = Beckman Coulter Genomics
    * Catalog Number = A63881
    * Website = <https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm>
  * TruSeq ChIP Sample Prep Kit, Box A or B
    * Supplier = Illumina
    * Catalog Number = 15034288; 15034289
    * Website = <https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html>

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-edc2d8306e297f8231c6b6157b78c0da7124e81e%2Ftruseq-chip-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>SPB Dilution</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 'step.::Total Number of Samples:: = step.::Total Number of Samples:: + 1' -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'if(input.::Target Insert Size (bp):: == 350) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 109.25) / 1000} ; if(input.::Target Insert Size (bp):: == 350) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 74.75) / 1000 } ; if(input.::Target Insert Size (bp):: == 550) { step.::SPB (ml):: = (step.::Total Number of Samples:: * 92) / 1000} ; if(input.::Target Insert Size (bp):: == 550) { step.::PCR Grade Water (ml):: = (step.::Total Number of Samples:: * 92) / 1000 } ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -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      | Well           | Built-in       |             |                                           |
    | Derived Sample | Sample Name    | Built-in       |             |                                           |
    | Derived Sample | Waiting        | Built-in       |             |                                           |
  * Expanded View Fields

    | **Category** | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container    | LIMS ID (Container) | Built-in       |             |                                           |
    | Project      | Project Name        | Built-in       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**     | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------ | -------------- | ----------- | ----------------------------------------- |
  | Comment            | Multiline Text |             |                                           |
  | 80% EtOH Prep Date | Date           |             |                                           |
* Step File Placeholders
  * Next Step 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 3: Adenylate 3' Ends (TruSeq ChIP-Seq v1.0)

* Master Step Name = Adenylate 3' Ends v2.0
* Step Type = No Outputs
* Reagent Kits
  * TruSeq ChIP Sample Prep Kit, Box A or B
    * Supplier = Illumina
    * Catalog Number = 15034288; 15034289
    * Website = <https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html>

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-814d7df28e62144f8008656f9e4e5c1af7ecc791%2Ftruseq-chip-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      | Well           | Built-in       |             |                                           |
    | Derived Sample | Sample Name    | Built-in       |             |                                           |
    | Derived Sample | Waiting        | Built-in       |             |                                           |
  * Expanded View Fields

    | **Category** | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container    | LIMS ID (Container) | Built-in       |             |                                           |
    | Project      | Project Name        | Built-in       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**         | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ---------------------- | -------------- | ----------- | ----------------------------------------- |
  | Comment                | Multiline Text |             |                                           |
  | Thermal Cycler Program | Text           |             | Default = ATAIL70                         |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * Well Sort Order = Column
  * Table Columns - Global Fields

    | **Category**   | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 4: Ligate Indexed Paired-End Adapters (TruSeq ChIP-Seq v1.0)

* Master Step Name = Ligate Adapters v2.0
* Step Type = Add Labels
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
  * AMPure XP Beads
    * Supplier = Beckman Coulter Genomics
    * Catalog Number = A63881
    * Website = <https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm>
  * TruSeq ChIP Sample Prep Kit, Box A or B
    * Supplier = Illumina
    * Catalog Number = 15034288; 15034289
    * Website = <https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html>

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-b970314b6a6ef6998080ae88bc561109572b9537%2Ftruseq-chip-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>

<details>

<summary>Copy to Output</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.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::' -log {compoundOutputFileLuid0}"
```

{% endcode %}

</details>

<details>

<summary>Set Next Step &#x26; Copy to Input</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 'nextStep = ::ADVANCE:: ; output.::Target Insert Size (bp):: = input.::Target Insert Size (bp)::'  -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      | Well           | Built-in       |             |                                           |
    | Derived Sample | Sample Name    | Built-in       |             |                                           |
    | Derived Sample | Waiting        | Built-in       |             |                                           |
  * Expanded View Fields

    | **Category** | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container    | LIMS ID (Container) | Built-in       |             |                                           |
    | Project      | Project Name        | Built-in       |             |                                           |

#### Add Labels

* Label Groups
  * TruSeq ChIP

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**     | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | ------------------ | -------------- | ----------- | ----------------------------------------- |
  | Comment            | Multiline Text |             |                                           |
  | 80% EtOH Prep Date | Date           |             |                                           |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * Well Sort Order = Row
  * Table Columns - Global Fields

    | **Category**   | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Reagent Name        | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 5: Purify Ligation Products (TruSeq ChIP-Seq v1.0)

* Master Step Name = Purify Ligation Products (TruSeq ChIP-Seq v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
  * 6X gel loading dye
    * Supplier = BioLabs
    * Catalog Number = B7021S
  * 50 bp DNA ladder
    * Supplier = NEB
    * Catalog Number = N3236L
  * 50X TAE buffer
    * Supplier = Bio-Rad
    * Catalog Number = 161-0743
  * 100bp DNA ladder
    * Supplier = NEB
    * Catalog Number = N3231L
  * Certified low-range ultra agarose
    * Supplier = Bio-Rad
    * Catalog Number = 161-3107
  * MinElute Gel Extraction Kit
    * Supplier = QIAGEN, part # 28604
    * Catalog Number = 28604
  * SYBR Gold Nucleic acid gel stain
    * Supplier = Invitrogen
    * Catalog Number = S11494
  * TruSeq ChIP Sample Prep Kit, Box A or B
    * Supplier = Illumina
    * Catalog Number = 15034288; 15034289
    * Website = <https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html>

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-2a4a7ebf319e2d92333876db9929ec0f0708ac50%2Ftruseq-chip-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      | Well           | Built-in       |             |                                           |
    | Derived Sample | Sample Name    | Built-in       |             |                                           |
    | Derived Sample | Waiting        | Built-in       |             |                                           |
  * Expanded View Fields

    | **Category** | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container    | LIMS ID (Container) | Built-in       |             |                                           |
    | Project      | Project Name        | Built-in       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
  | -------------- | -------------- | ----------- | ----------------------------------------- |
  | Comment        | Multiline Text |             |                                           |
* Step File Placeholders
  * Log File - Automatically attached
  * Gel Image - Manually uploaded
* Sample Table
  * Sample Display Default = Expand
  * Well Sort Order = Row
  * Table Columns - Global Fields

    | **Category**   | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 6: Enrich DNA Fragments (TruSeq ChIP-Seq v1.0)

* Master Step Name = Enrich DNA Fragments (TruSeq ChIP-Seq v1.0)
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {SubmittedSampleName}
* Reagent Kits
  * AMPure XP Beads
    * Supplier = Beckman Coulter Genomics
    * Catalog Number = A63881
    * Website = <https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/agencourt-ampure-xp-pcr-purification/index.htm>
  * TruSeq ChIP Sample Prep Kit, Box A or B
    * Supplier = Illumina
    * Catalog Number = 15034288; 15034289
    * Website = <https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-chip.html>
  * TruSeq ChIP Sample Prep Kit, PCR Box
    * Supplier = Illumina
    * Catalog Number = 15027084

#### Automations

<figure><img src="https://2084401275-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FfjuebS41N49G1Eh55hP7%2Fuploads%2Fgit-blob-237a5cc65eeeb035b777fd4724afe05e8ceee677%2Ftruseq-chip-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      | Well           | Built-in       |             |                                           |
    | Derived Sample | Sample Name    | Built-in       |             |                                           |
    | Derived Sample | Waiting        | Built-in       |             |                                           |
  * Expanded View Fields

    | **Category** | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container    | LIMS ID (Container) | Built-in       |             |                                           |
    | Project      | Project Name        | Built-in       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**         | **Field Type** | **Options** | **Additional Options and Dropdown Items**                           |
  | ---------------------- | -------------- | ----------- | ------------------------------------------------------------------- |
  | Comment                | Multiline Text |             |                                                                     |
  | Number of PCR Cycles   | Numeric        |             | <ul><li>Default = 18</li><li>Decimal Places Displayed = 0</li></ul> |
  | Thermal Cycler Program | Text           |             | <ul><li>Default = PCR</li></ul>                                     |
  | 80% EtOH Prep Date     | Date           |             |                                                                     |
* Step File Placeholders
  * Log File - Automatically attached
* Sample Table
  * Sample Display Default = Expand
  * Well Sort Order = Row
  * Table Columns - Global Fields

    | **Category**   | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | -------------- | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container      | Container Name      | Built-in       |             |                                           |
    | Container      | LIMS ID (Container) | Built-in       |             |                                           |
    | Container      | Well                | Built-in       |             |                                           |
    | Derived Sample | Sample Name         | Built-in       |             |                                           |
    | Project        | Project Name        | Built-in       |             |                                           |

### Step 7: Bioanalyzer QC (Library Validation) (TruSeq ChIP-Seq v1.0)

* 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-9ba86c1b3f56fa412369f5ded6d024e245cbbccb%2Ftruseq-chip-step7-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, Copy 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 '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>

<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, 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>

#### 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 ChIP-Seq 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 8: Normalize Libraries (TruSeq ChIP-Seq v1.0)

* Master Step Name = Normalize Libraries 2 v2.0.10
* Step Type = Standard
* Derived Sample Generation = Fixed, 1
* Naming Convention = {InputItemName}

{% hint style="info" %}
The version of Normalized Libraries 2 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-53aa43be6d887755747657cc53208ff10ab19a1c%2Ftruseq-chip-step8-automation.png?alt=media" alt=""><figcaption></figcaption></figure>

<details>

<summary>Normalization Calculations - Option 2</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:http} -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.::Sample Volume (ul):: ; output.::Buffer Volume (ul):: = 0 ; output.::Normalized Molarity (nM):: = output.::Molarity (nM)::} else {output.::Sample Volume (ul):: = step.::Sample Volume (ul):: ; output.::Buffer Volume (ul):: = ((output.::Molarity (nM):: * step.::Sample Volume (ul)::) / step.::Target Normalization (nM)::) - step.::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 the 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      | Well           | Built-in       |             |                                           |
    | Derived Sample | Sample Name    | Built-in       |             |                                           |
    | Derived Sample | Waiting        | Built-in       |             |                                           |
  * Expanded View Fields

    | **Category** | **Field Name**      | **Field Type** | **Options** | **Additional Options and Dropdown Items** |
    | ------------ | ------------------- | -------------- | ----------- | ----------------------------------------- |
    | Container    | LIMS ID (Container) | Built-in       |             |                                           |
    | Project      | Project Name        | Built-in       |             |                                           |

#### Record Details

* Step Data (Master Step Fields)

  | **Field Name**            | **Field Type** | **Options**    | **Additional Options and Dropdown Items**                           |
  | ------------------------- | -------------- | -------------- | ------------------------------------------------------------------- |
  | Comment                   | Multiline Text |                |                                                                     |
  | Sample Volume (ul)        | Numeric        | Required Field | <ul><li>Default = 10</li><li>Decimal Places Displayed = 0</li></ul> |
  | Target Normalization (nM) | Numeric        | Required Field | <ul><li>Default = 10</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 | Molarity (nM)            | Numeric        |                | Decimal Places Displayed = 2                                                                                                                                                                         |
    | Derived Sample | Buffer Volume (ul)       | Numeric        |                | Decimal Places Displayed = 2                                                                                                                                                                         |
    | Derived Sample | Normalized Molarity (nM) | Numeric        |                | Decimal Places Displayed = 2                                                                                                                                                                         |
    | Derived Sample | Sample Name              | Built-in       |                |                                                                                                                                                                                                      |
    | Derived Sample | Sample Volume (ul)       | Numeric        |                | Decimal Places Displayed = 2                                                                                                                                                                         |
    | Derived Sample | Sequencing Instrument    | Text Dropdown  | Required Field | <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 by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/clarity-lims/library-prep/truseq/truseq-chip-seq-v1.0.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

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