Illumina Preset Protocol - GenomeStudio

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)

Protocol Type: Other

Master Step 1: Create Infinium Genotyping Analysis SampleSheet - GenomeStudio

Step Type: No Output

Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Master Step Fields

BeadPool Manifest

Text

  
 

Multiline Text Fields

Comment

Multiline Text

  

Step File Placeholders

 

File Name

GenomeStudio Genotyping Sample Sheet

Auto
     

File Generation Log

Auto
     

Log

Auto

Sample Table

Table Columns

Infinium Kit Name

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

BeadChip Barcode

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

BeadChip Position

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

DNA Plate Barcode

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

Sample_Well

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

Array Secondary Analysis

Text
• Global field - derived sample
• Required
• Calculated - copied from step
Automation

Automation Name

Setting

Value

Specification

Generate GenomeStudio Genotyping Sample Sheet

Trigger Location

Record Details

  
 

Trigger Style

Manual

  
     

Command line

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_SampleSheet_driver_file.csv -o {compoundOutputFileLuid0}.csv -l {compoundOutputFileLuid1}"

Set Next Step - Remove

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

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}"

Mark Protocol Complete

Protocol 2: Infinium Methylation Analysis (GenomeStudio)

Protocol Type: Other

Master Step 1: Create Infinium Methylation Analysis SampleSheet - GenomeStudio

Step Type: No Output

Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Comment

Multiline Text

  

Step File Placeholders

 

File Name

GenomeStudio Methylation Sample Sheet

Auto
     

File Generation Log

Auto
     

Log

Auto

Sample Table

Table Columns

Infinium Kit Name

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

BeadChip Barcode

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

BeadChip Position

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

DNA Plate Barcode

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

Sample_Well

Text
• Global field - derived sample
• Required
• Calculated - copied from step
   

Array Secondary Analysis

Text
• Global field - derived sample
• Required
• Calculated - copied from step
Automation

Automation Name

Setting

Value

Specification

Generate GenomeStudio Genotyping Sample Sheet

Trigger Location

Record Details

  
 

Trigger Style

Manual

  
     

Command line

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}"

Set Next Step - Advance

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

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}"

 

Mark Protocol Complete