Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

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2 Chapter 2 Prepare Run Settings Set analysis parameters – Color balance – Quality value – Blur value – Blur population – Exposure value – Exposure population – Exposure time Note: Refer to “Primary analysis parameters” on page 25 for details on these parameters. 24 Applied Biosystems SOLiD 4 System SETS Software User Guide
Primary analysis parameters 5. Click Save to keep the new settings. Applied Biosystems SOLiD 4 System SETS Software User Guide Chapter 2 Prepare Run Settings Set analysis parameters 2 Note: Click Restore Defaults at any time to reestablish the original (and recommended) default settings for primary analysis. Primary analysis parameters control the traffic light “signals,” or thresholds that you will use in determining the quality of a run cycle, even to stop a run midstream if the traffic lights signal a poor quality run cycle. The value for each setting is accessible in SETS and modifications can be made to increase or decrease each value for a custom run setting. Target values for parameters Parameter Stringency 20 Panel Alignment ≥90% HQ Beads ≥35% Bead Retention ≥95% Color Balance ≤3% QV Median ≥20 Blur Value ≤2.2 Blur Population ≤75% Exposure Value ≤0.05 Exposure Population 0 Exposure Time ≤200 Target Value for Primary Analysis 25
Page 1 and 2: Applied Biosystems SOLiD 4 System
Page 7 and 8: How to use this guide Applied Biosy
Page 9 and 10: 1 �� SETS So
Page 11 and 12: Naming convention for sequencing re
Page 13 and 14: SETS homepage Applied Biosystems SO
Page 19 and 20: SOLiD 4 System Software workflow A
Page 21 and 22: Log in to SETS Applied Biosystems S
Page 23: Define primary analysis settings Ap
Page 27 and 28: Parameter Description Applied Biosy
Page 29 and 30: Parameter Description Applied Biosy
Page 31 and 32: Parameter Description Application D
Page 33 and 34: Define secondary analysis settings
Page 35 and 36: Chapter 2 Prepare Run Settings Set
Page 37 and 38: Load a Reference Sequence Specify a
Page 43 and 44: Note: For in-progress runs, you can
Page 45 and 46: Note: Refer to the Imaging Metrics
Page 47 and 48: Chapter 3 Monitor the Run in SETS V
Page 49 and 50: View sample data Applied Biosystems
Page 51 and 52: Troubleshoot failed jobs Sample ana
Page 53 and 54: Colorcall Jobs Applied Biosystems S
Page 55 and 56: Filter Fasta fails Applied Biosyste
Page 57 and 58: View History View Run History in SE
Page 61 and 62: System Logs Applied Biosystems SOLi
Page 65 and 66: Imaging Metrics Report Applied Bios
Page 67 and 68: Cycle Heat Map Report Select a heat
Page 69 and 70: Chapter 4 View Reports View overall
Page 71 and 72: Exposure Time Report Applied Biosys
Page 73 and 74: Chapter 4 View Reports View overall
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Determine the optimal titration poi
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View sample reports Applied Biosyst
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Resizing images Applied Biosystems
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Scaled data Applied Biosystems SOLi
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Angle data Applied Biosystems SOLiD
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View Analysis Reports Applied Biosy
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View analysis Data Files View Analy
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Auto-Correlation Report Applied Bio
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Error Profiles Report Applied Biosy
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Master Report Tool Generate a Maste
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Chapter 4 View Reports Master Repor
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5 �� SETS So
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Chapter 5 Perform Reanalysis Primar
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Effect on the current run Applied B
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6 �� SETS So
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View Multiplexing Series in SETS Ac
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Set up Multiplexing run in ICS Crea
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Multiplexing Assignment report Appl
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Reassign Run Applied Biosystems SOL
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7 �� SETS So
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Auto export in SETS Applied Biosyst
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Auto export with JMS broker and Exp
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3. Run the following command: Appli
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Manually configure the RSA keys App
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Change export for current run only
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Event notifications and email servi
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Applied Biosystems SOLiD 4 System
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Delete runs Applied Biosystems SOLi
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Chapter 7 Manage Administrative Tas
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A Overview Applied Biosystems SOLiD
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Appendix A Web Services WSDL A Bind
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B Applied Biosystems SOLiD 4 Syste
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Appendix B Advanced Topic: Data Ana
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Appendix B Advanced Topic: Data Ana
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Complementing color-space data Appl
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Data analysis considerations Unders
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SNPs and errors High accuracy for S
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Sampling Allele ratio Applied Biosy
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C Saving data Applied Biosystems SO
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D What is primary analysis? Applied
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Primary analysis workflow Applied B
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Primary analysis inputs and outputs
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Appendix D Advanced Topic: Primary
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Storage requirements for primary an
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Redo the read-filtering process App
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Image metrics Applied Biosystems SO
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Usage Validation and observed quali
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Key files generated by primary anal
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.spch files Applied Biosystems SOLi
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Troubleshooting analysis failure Ap
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E Applied Biosystems SOLiD 4 Syste
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LICENSE Appendix E Software License
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Appendix E Software License Agreeme
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Alignment Matrix The alignment matr
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Glossary WFA A Workflow Analysis (W
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Related documentation Document BioS
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Part Number 4448411 Rev. B 04/2010
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