> 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/ilass-and-infinium-arrays/infinium-arrays/infinium-genome-studio-v1.0.md). # GenomeStudio v1.0 ## Overview The GenomeStudio workflow includes the following functionality. * Automatic Generation of a sample sheet for genotyping or methylation. These sample sheets can then be used in GenomeStudio to create a project. ## Protocol 1: Infinium Genotyping Analysis (GenomeStudio v1.0) Protocol Type = Sample Analysis **Next Steps Configuration**
### Step 1: Create Infinium Genotyping Analysis Sample Sheet (GenomeStudio v1.0) * Master Step Name = Create Infinium Genotyping Analysis Sample Sheet - GenomeStudio v1.0 * Step Type = No Outputs #### Automations
Generate GenomeStudio Genotyping Sample Sheet * 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/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/driverfiletemplates/genomeStudio_Genotyping_SampleSheet_driver_file.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue * 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 | Infinium Kit Name | Text | Read Only | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Waiting | Built-in | | | | Project | Project Name | Built-in | | | #### 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 | Infinium Kit Name | Text | Read Only | | | 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** | | ----------------- | -------------- | -------------- | ----------------------------------------- | | BeadPool Manifest | Text | Required Field | | | Comment | Multiline Text | | | * Step File Placeholders * GenomeStudio Genotyping Sample Sheet - Automatically attached * File Generation Log - Automatically attached * Log - Automatically attached * Sample Table * Sample Display Default = Collapse * Well Sort Order = Row * Table Columns - Global Fields | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ------------------------ | -------------- | ----------- | ---------------------------------------------------------------------------------------------------------------------- | | Derived Sample | Array Secondary Analysis | Text Dropdown | | | | Derived Sample | BeadChip Barcode | Text | Read Only | | | Derived Sample | BeadChip Position | Text | Read Only | | | Derived Sample | DNA Plate Barcode | Text | Read Only | | | Derived Sample | Infinium Kit Name | Text | Read Only | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample\_Well | Text | | | | Project | Project Name | Built-in | | | ## Protocol 2: Infinium Methylation Analysis (GenomeStudio v1.0) Protocol Type = Data Analysis **Next Steps Configuration**
### Step 1: Create Infinium Methylation Analysis Sample Sheet (GenomeStudio v1.0) * Master Step Name = Create Infinium Methylation Analysis Sample Sheet - GenomeStudio v1.0 * Step Type = No Outputs #### Automations
Generate GenomeStudio Methylation Sample Sheet * 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/DriverFileGenerator.jar script:driver_file_generator -i {processURI:v2} -u {username} -p {password} -t /opt/gls/clarity/extensions/conf/driverfiletemplates/genomeStudio_Methylation_SampleSheet_driver_file.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}" ``` {% endcode %}
Set Next Step - Advance * Trigger Location = Record Details * Trigger Style = Automatic upon exit {% code overflow="wrap" %} ```markup bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'nextStep = ::ADVANCE::' \ -log {compoundOutputFileLuid0}" ``` {% endcode %}
#### Queue/Ice Bucket * Defaults * Sample Grouping = Group by Containers * Well Sort Order = Row * Sample Table (Column Headers) | **Category** | **Field Name** | **Field Type** | **Options** | **Additional Options and Dropdown Items** | | -------------- | ----------------- | -------------- | ----------- | ----------------------------------------- | | Container | Container Name | Built-in | | | | Container | Well | Built-in | | | | Derived Sample | Infinium Kit Name | Text | Read Only | | | 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 | | | * Step File Placeholders * GenomeStudio Methylation Sample Sheet - Automatically attached * File Generation Log - Automatically attached * Log - Automatically attached * Sample Table * Sample Display Default = Collapse * 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 | Array Secondary Analysis | Text Dropdown | | | | Derived Sample | BeadChip Barcode | Text | Read Only | | | Derived Sample | BeadChip Position | Text | Read Only | | | Derived Sample | DNA Plate Barcode | Text | Read Only | | | Derived Sample | Infinium Kit Name | Text | Read Only | | | Derived Sample | Sample Name | Built-in | | | | Derived Sample | Sample\_Well | Text | | | | Project | Project Name | Built-in | | | --- # 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/ilass-and-infinium-arrays/infinium-arrays/infinium-genome-studio-v1.0.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.