RNA Library Prep v1.1 Protocol 1: RNA Library Prep (AmpliSeq for Illumina Focus Panel v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Dilute RNA (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Dilute RNA (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Group of Defaults
chevron-right hashtag Directions = If enough RNA is available, dilute to intermediate concentration ~20-1000 ng/uL.
chevron-right hashtag Default = If enough RNA is available, dilute to intermediate concentration ~20-1000 ng/uL.
Step Data
Group of Defaults = Immune Repertoire Panel
Step 2: Qubit (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Qubit (AmpliSeq for Illumina v1.1)
Measurement Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 3: Dilute RNA (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Dilute RNA (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 4: Reverse Transcribe (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Reverse Transcribe RNA (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Group of Defaults
chevron-right hashtag AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
chevron-right hashtag AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
chevron-right hashtag AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
chevron-right hashtag AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
chevron-right hashtag AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
chevron-right hashtag AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
chevron-right hashtag AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
chevron-right hashtag AmpliSeq ERCC RNA Spike-in Mix = No
Directions = If RNA was prepared from FFPE tissue and never heat-treated, heat at 80°C for 10 minutes and then cool to room temperature before proceeding to reverse transcription.
Step Data
Group of Defaults = Focus Panel
Step 5: Amplify cDNA Targets (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Amplify cDNA Targets (AmpliSeq for Illumina Focus Panel v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
chevron-right hashtag Trigger Location = Not Used
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 6: Partially Digest Amplicons (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Partially Digested Amplicons (AmpliSeq for Illumina Focus Panel v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Desired Concentration (ng/uL)
Default = If enough RNA is available, dilute to intermediate concentration ~20-50 ng/uL.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Criteria 1 - Threshold Value
Criteria 2 - Source Data Field
Criteria 2 - Threshold Value
Step File Placeholders
Log - Automatically attached
QC Log File - Automatically attached
QC Result File - Automatically attached
Upload File - Manually uploaded
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Default = If enough RNA is available, dilute to intermediate concentration ~20-50 ng/uL.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq cDNA Synthesis for Illumina
Catalog Number = 20022654
AmpliSeq Focus Panel for RNA
Catalog Number = 20019164
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Prep Input Amount (ng) = 20
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA per pool. The recommended input is 10 ng RNA per pool.
Thermal Cycler Program = RT
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Prep Input Amount (ng) = 1000
Recommended Prep Input (ng) = Each reaction requires 10-1000 ng of DNase-treated total RNA. If RNA is not limiting, the recommended input is 1000 ng RNA. High RNA input amounts are recommended for rare clones.
Thermal Cycler Program = RT
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 10-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Prep Input Amount (ng) = 1000
Recommended Prep Input (ng) = Each reaction requires 50-1000 ng of DNase-treated total RNA. If RNA is not limited, the recommended input is 1000 ng RNA
Thermal Cycler Program = RT
Prep Input Amount (ng) = 10
Recommended Prep Input (ng) = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Thermal Cycler Program = RT
Additional Options and Dropdown Items
5X AmpliSeq cDNA Reaction Mix (uL)
Decimal Places Displayed = 1
10X AmpliSeq RT Enzyme Mix (uL)
Decimal Places Displayed = 1
Desired Concentration (ng/uL)
Decimal Places Displayed = 1
Decimal Places Displayed = 2
Recommended Prep Input (ng)
Default = Each reaction requires 1-100 ng of DNase-treated total RNA. The recommended input is 10 ng RNA.
Decimal Places Displayed = 0
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Focus Panel for RNA
Catalog Number = 20019164
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Sample Table (Column Headers)
Additional Options and Dropdown Items
Decimal Places Displayed = 1
Decimal Places Displayed = 1
Decimal Places Displayed = 1
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq cDNA Synthesis for Illumina
Catalog Number = 20022654
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Additional Options and Dropdown Items
Desired Concentration (ng/uL)
Additional Options and Dropdown Items
5x AmpliSeq Focus Panel (uL)
Decimal Places Displayed = 1
5X AmpliSeq HiFi Mix (uL)
Additional Options and Dropdown Items
Copy 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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"
Copy 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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \
output.::Nuclease-free water (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Total Volume (uL):: ' \
-log {compoundOutputFileLuid0}"
Copy 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.::Desired Concentration (ng/uL):: = step.::Desired Concentration (ng/uL)::' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"
Copy 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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"
Copy 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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"
Copy 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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \
output.::Nuclease-free water (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Total Volume (uL):: ' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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.::Desired Concentration (ng/uL):: = step.::Desired Concentration (ng/uL)::' \
-log {compoundOutputFileLuid0}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Concentration:: = input.::Concentration:: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
output.::Total Volume (uL):: = input.::Total Volume (uL):: ; \
output.::Input Amount (ng):: = input.::Input Amount (ng):: ; \
step.::Desired Concentration (ng/uL):: = input.::Desired Concentration (ng/uL)::' \
-log {compoundOutputFileLuid0}"
Copy 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 'step.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
if (step.::Prep Input Volume (uL):: < 7) {step.::Nuclease-free water (uL):: = (7 - step.::Prep Input Volume (uL)::) * step.::Total Samples::*1.1} else {step.::Nuclease-free water (uL):: = 0} ; \
step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 2; \
step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 1' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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 'step.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
if (step.::Prep Input Volume (uL):: < 7) {step.::Nuclease-free water (uL):: = (7 - step.::Prep Input Volume (uL)::) * step.::Total Samples::*1.1} else {step.::Nuclease-free water (uL):: = 0} ; \
step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 2 ; \
step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 1' \
-log {compoundOutputFileLuid0}"
Copy 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 'step.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
if (step.::Prep Input Volume (uL):: < 3.5) {step.::Nuclease-free water (uL):: = (3.5 - step.::Prep Input Volume (uL)::) * step.::Total Samples::*1.1} else {step.::Nuclease-free water (uL):: = 0} ; \
step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 1 ; \
step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 0.5' \
-log {compoundOutputFileLuid0}"
Copy 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 'step.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
if (step.::Prep Input Volume (uL):: < 7.0) {step.::Nuclease-free water (uL):: = (7.0 - (step.::Prep Input Volume (uL):: + output.::AmpliSeq ERCC RNA Spike-in Volume (uL)::)) * step.::Total Samples::*1.1} else {step.::Nuclease-free water (uL):: = 0} ; \
step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 1 ; \
step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 0.5 ; \
step.::AmpliSeq ERCC RNA Spike-in Mix (uL):: = step.::Total Samples:: * output.::AmpliSeq ERCC RNA Spike-in Volume (uL):: *1.1' \
-log {compoundOutputFileLuid0}"
Copy 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 'step.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
if (step.::Prep Input Volume (uL):: < 3.5) {step.::Nuclease-free water (uL):: = (3.5 - step.::Prep Input Volume (uL)::) * step.::Total Samples::*1.1} else {step.::Nuclease-free water (uL):: = 0} ; \
step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 1 ; \
step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 0.5' \
-log {compoundOutputFileLuid0}"
Copy 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 'step.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
if (step.::Prep Input Volume (uL):: < 7) {step.::Nuclease-free water (uL):: = (7 - step.::Prep Input Volume (uL)::) * step.::Total Samples::*1.1} else {step.::Nuclease-free water (uL):: = 0} ; \
step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 2 ; \
step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 1' \
-log {compoundOutputFileLuid0}"
Copy 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 'step.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
if (step.::Prep Input Volume (uL):: < 3.5) {step.::Nuclease-free water (uL):: = (3.5 - (step.::Prep Input Volume (uL):: + output.::AmpliSeq ERCC RNA Spike-in Volume (uL)::)) * step.::Total Samples::*1.1} else {step.::Nuclease-free water (uL):: = 0} ; \
step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 1 ; \
step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 0.5 ; \
step.::AmpliSeq ERCC RNA Spike-in Mix (uL):: = step.::Total Samples:: * output.::AmpliSeq ERCC RNA Spike-in Volume (uL):: *1.1' \
-log {compoundOutputFileLuid0}"
Copy 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 'step.::Prep Input Volume (uL):: = step.::Prep Input Amount (ng):: / step.::Desired Concentration (ng/uL):: ; \
if (step.::Prep Input Volume (uL):: < 7) {step.::Nuclease-free water (uL):: = (7 - step.::Prep Input Volume (uL)::) * step.::Total Samples::*1.1} else {step.::Nuclease-free water (uL):: = 0} ; \
step.::5X AmpliSeq cDNA Reaction Mix (uL):: = step.::Total Samples:: * 1.1 * 2; \
step.::10X AmpliSeq RT Enzyme Mix (uL):: = step.::Total Samples:: * 1.1 * 1' \
-log {compoundOutputFileLuid0}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Concentration:: = input.::Desired Concentration (ng/uL):: ; \
output.::Conc. Units:: = input.::Conc. Units:: ; \
output.::Total Volume (uL):: = input.::Total Volume (uL):: ; \
output.::Input Amount (ng):: = input.::Input Amount (ng):: ; \
step.::Desired Concentration (ng/uL):: = input.::Desired Concentration (ng/uL)::' \
-log {compoundOutputFileLuid0}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Sample Type:: = ::cDNA:: ; \
step.::5X AmpliSeq HiFi Mix (uL):: = 4 * step.::Total Samples:: * 1.1 ; \
step.::5x AmpliSeq Focus Panel (uL):: = 4 * step.::Total Samples:: * 1.1 ; \
step.::Nuclease-free water (uL):: = 2 * step.::Total Samples:: * 1.1' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Sample Type' \
--FIELD_VALUE 'cDNA' \
--WORKFLOW 'DNA Library Prep AmpliSeq for Illumina Childhood Cancer Panel v1.1' \
--STEP 'Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Childhood Cancer Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Sample Type:: = ::cDNA:: ; \
step.::5X AmpliSeq HiFi Mix (uL):: = 4 * step.::Total Samples:: * 1.1 ; \
step.::Nuclease-free water (uL):: = 2 * step.::Total Samples:: * 1.1' \
-log {compoundOutputFileLuid0}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'output.::Sample Type:: = ::cDNA:: ; \
step.::5X AmpliSeq HiFi Mix (uL):: = 4.0 * step.::Total Samples:: * 1.1 ; \
step.::5X AmpliSeq Immune Repertoire Panel (uL):: = 4.0 * step.::Total Samples:: * 1.1 ; \
step.::Nuclease-free water (uL):: = 7.0 * step.::Total Samples:: * 1.1' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Queue for Plate Transfer' \
--FIELD_VALUE 'Transfer Amplicons' \
--WORKFLOW 'DNA Library Prep AmpliSeq for Illumina Focus Panel v1.1' \
--STEP 'Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Focus Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' " Desired Concentration (ng/uL)
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Default = Transfer Amplicons
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Standard v1.1 Protocol 1: Standard Workflow (AmpliSeq for Illumina Focus Panel v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Amplify Library (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Group of Defaults
chevron-right hashtag Thermal Cycler Program = AMP
chevron-right hashtag Thermal Cycler Program = EQUAL
chevron-right hashtag Thermal Cycler Program = AMP_7
Step Data
Group of Defaults = Standard Workflow
Step 3: Perform Second Clean Up (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Perform Second Clean Up (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Agencourt AMPure XP Beads
Catalog Number = NC9959336; NC9933872
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Sample Table (Column Headers)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Decimal Places Displayed = 2
10X Library Amp Primers (uL)
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
Agencourt AMPure XP Beads
Catalog Number = NC9959336; NC9933872
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Copy 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}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::1X Lib AMP Mix (uL):: = step.::Total Samples:: * 1.1 * 45 ; \
step.::10X Library Amp Primers (uL):: = step.::Total Samples:: * 1.1 * 5' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \ -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \ step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \ -log {compoundOutputFileLuid0}"
Copy 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}" Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Equalizer v1.1 Protocol 1: Equalizer Workflow (AmpliSeq for Illumina Focus Panel v1.1)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Clean Up Library (AmpliSeq for Illumina v1.1)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Amplify Library (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Amplify Library (AmpliSeq for Illumina v1.1)
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Group of Defaults
chevron-right hashtag Thermal Cycler Program = AMP
chevron-right hashtag Thermal Cycler Program = EQUAL
chevron-right hashtag Thermal Cycler Program = AMP_7
Step Data
Group of Defaults = Equalizer Workflow
Step 3: Perform Capture and Clean Up (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Perform Capture and Clean Up (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step File Placeholders
Log - Automatically attached
Step 4: Elute Library (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Elute Library (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Agencourt AMPure XP Beads
Catalog Number = NC9959336; NC9933872
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Sample Table (Column Headers)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Decimal Places Displayed = 2
10X Library Amp Primers (uL)
Decimal Places Displayed = 2
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Column
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Copy 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}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \
-log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \
script:evaluateDynamicExpression \
-t false \
-h false \
-exp 'step.::1X Lib AMP Mix (uL):: = step.::Total Samples:: * 1.1 * 45 ; \
step.::10X Library Amp Primers (uL):: = step.::Total Samples:: * 1.1 * 5' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::Total Samples:: = step.::Total Samples:: + 1' \ -log {compoundOutputFileLuid0} && /opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2} -u {username} -p {password} \ script:evaluateDynamicExpression \ -t false \ -h false \ -exp 'step.::1X Lib Amp Mix:: = step.::Total Samples:: * 1.1 * 45 ; \ step.::10X Library Amp Primers:: = step.::Total Samples:: * 1.1 * 5' \ -log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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}" Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
DNA Library Prep v1.1 Protocol 1: DNA Library Prep (AmpliSeq for Illumina Focus Panel v1.1)
Protocol Type = Library Prep
Next Steps Configuration
Step 1: Dilute DNA (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Not Used
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 2: Qubit (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Qubit (AmpliSeq for Illumina v1.1)
Measurement Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 3: Dilute DNA to Final Concentration (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Dilute DNA (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 4: Amplify Targets (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Amplify Targets (AmpliSeq for Illumina Focus Panel)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon entry
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Manual button
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 5: Partially Digested Amplicons (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Partially Digested Amplicons (AmpliSeq for Illumina Focus Panel v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Step Data (Master Step Fields)
Step 6: Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Transfer RNA and DNA Amplicons (AmpliSeq for Illumina)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Step File Placeholders
Log - Automatically attached
Step 7: Ligate Indexes (AmpliSeq for Illumina Focus Panel v1.1)
Master Step Name = Ligate Indexes (AmpliSeq for Illumina v1.1)
Derived Sample Generation = Fixed, 1
chevron-right hashtag Trigger Location = Record Details
Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Style = Automatic upon exit
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
chevron-right hashtag Trigger Location = Not Used
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Label Groups
AmpliSeq CD Indexes Set A for Illumina
AmpliSeq CD Indexes Set B for Illumina
Step Data (Master Step Fields)
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Criteria 1 - Threshold Value
Criteria 2 - Source Data Field
Criteria 2 - Threshold Value
Step File Placeholders
Log - Automatically attached
QC Log File - Automatically attached
QC Result File - Automatically attached
Upload File - Manually uploaded
Sample Table
Sample Display Default = Expand
File Column Options
File Column Display = Hide
File Attachment Method = Auto
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Focus Panel for DNA
Catalog Number = 20019164
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
Sample Table (Column Headers)
Additional Options and Dropdown Items
Default = This protocol supports 1-1000 ng. The recommended input is 100 ng high-quality DNA.
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq cDNA Synthesis for Illumina
Catalog Number = 20022654
Sample Table (Column Headers)
Additional Options and Dropdown Items
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Naming Convention = {InputItemName}
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Naming Convention = {InputItemName}
Reagent Kits
AmpliSeq Library PLUS for Illumina
Catalog Number = 24 - 20019101; 96 - 200191102; 384 - 200191103
ℹ The workflow version and step version for the routing script may vary depending on the version of the IPP.
Sample Table (Column Headers)
Additional Options and Dropdown Items
Placement Pattern = Row
AmpliSeq CD Indexes Set C for Illumina
AmpliSeq CD Indexes Set D for Illumina
AmpliSeq UD Indexes for Illumina (24 Indexes)
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Expand
Table Columns - Global Fields
Additional Options and Dropdown Items
Desired Concentration (ng/uL)
Decimal Places Displayed = 0
Additional Options and Dropdown Items
Criteria 1 - Source Data Field
Additional Options and Dropdown Items
Desired Concentration (ng/uL)
Decimal Places Displayed = 0
Additional Options and Dropdown Items
Decimal Places Displayed = 0
Recommended Prep Input (ng)
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Copy 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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"
Copy 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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Total Volume (uL):: ' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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:assignQC -log {compoundOutputFileLuid1} -qcResult {compoundOutputFileLuid2}"
Copy 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:: ; input.::Concentration:: = output.::Concentration:: ; input.::Conc. Units:: = output.::Conc. Units::' -log {compoundOutputFileLuid0}"
Copy 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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Sample Volume (uL):: = 5' \
-log {compoundOutputFileLuid0}"
Copy 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.::Total Volume (uL):: = (output.::Concentration::/step.::Desired Concentration (ng/uL)::) * output.::Sample Volume (uL):: ; \
output.::Low TE (uL):: = output.::Total Volume (uL):: - output.::Sample Volume (uL):: ; \
output.::Input Amount (ng):: = step.::Desired Concentration (ng/uL):: * output.::Total Volume (uL):: ' \
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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.::Concentration:: = input.::Concentration:: ; output.::Conc. Units:: = input.::Conc. Units:: ; output.::Total Volume (uL):: = input.::Total Volume (uL):: ; output.::Input Amount (ng):: = input.::Input Amount (ng):: ; output.::5X AmpliSeq HiFi Mix (uL):: = 4.0 ; output.::5x AmpliSeq Focus Panel (uL):: = 4.0'\
-log {compoundOutputFileLuid0}"
Copy 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.::Prep Input Volume (uL):: = output.::Prep Input Amount (ng):: / output.::Concentration:: ; \
if (output.::Prep Input Volume (uL):: < 12) {output.::Nuclease-free water (uL):: = 12 - output.::Prep Input Volume (uL)::} '\
-log {compoundOutputFileLuid0}"
Copy 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}"
Copy 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}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'Queue for Plate Transfer' \
--FIELD_VALUE 'Transfer Amplicons' \
--WORKFLOW 'DNA Library Prep AmpliSeq for Illumina Focus Panel v1.1' \
--STEP 'Transfer RNA and DNA Amplicons (AmpliSeq for Illumina Focus Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' "
Copy 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}"
Copy 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}"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Focus Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Focus Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Focus Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Immune Repertoire Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Repertoire Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina BRCA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina BRCA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina BRCA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Childhood Cancer Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Childhood Cancer Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Childhood Cancer Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Cancer HotSpot Panel V2 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Panel v3 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Comprehensive Panel v3 v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Comprehensive Panel v3 v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Custom DNA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Custom DNA Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Custom DNA Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Immune Response Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Immune Response Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Immune Response Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Myeloid Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Myeloid Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Myeloid Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'"
Copy bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -u {username} -p {password} -i {stepURI:v2} -l {compoundOutputFileLuid0} script:changeWorkflow \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Standard Workflow' \
--WORKFLOW 'Standard Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS' \
\
--FIELD_NAME 'AmpliSeq Workflow' \
--FIELD_VALUE 'Equalizer Workflow' \
--WORKFLOW 'Equalizer Workflow AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1' \
--STEP 'Clean Up Library (AmpliSeq for Illumina Transcriptome Human Gene Expression Panel v1.1)' \
--INPUTS_OR_OUTPUTS 'OUTPUTS'" Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Decimal Places Displayed = 2
5x AmpliSeq Focus Panel (uL)
Decimal Places Displayed = 1
5X AmpliSeq HiFi Mix (uL)
Decimal Places Displayed = 1
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 0
Decimal Places Displayed = 2
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Decimal Places Displayed = 2
Additional Options and Dropdown Items
Additional Options and Dropdown Items
Additional Options and Dropdown Items
