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

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Contents Chapter 5 Perform Reanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . 97 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 Primary reanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 Secondary reanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 Chapter 6 Support Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . 103 Fragment and Paired-End Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . 104 View Multiplexing Series in SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 Set up Multiplexing run in ICS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 Multiplexing Assignment Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 Reassign Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 Chapter 7 Manage Administrative Tasks . . . . . . . . . . . . . . . . . 113 Export Data with SOLiD 4 System Software . . . . . . . . . . . . . . . . . . . 114 Auto export in SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 Manual export in SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 Event notifications and email services . . . . . . . . . . . . . . . . . . . . . . . . . 125 Alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128 Delete runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 Manage Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 Appendix A Web Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 WSDL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134 Appendix B Advanced Topic: Data Analysis Overview . . . . . . . . 137 Fundamentals of color-space analysis . . . . . . . . . . . . . . . . . . . . . . . . . 137 The 2-base color coding scheme . . . . . . . . . . . . . . . . . . . . . . . . . 137 Color-coding process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138 Required properties for a 2-base color code scheme . . . . . . . . . . 141 How the system satisfies 2-base coding system requirements . . 142 Principles of ligation-based chemistry and 2-base encoding . . . . 143 4 Applied Biosystems SOLiD 4 System SETS Software User Guide
Applied Biosystems SOLiD 4 System SETS Software User Guide Contents Color-space and base space as applied in the SOLiD 4 System . . . . 145 Color-space data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 Relationship between cycle and base position . . . . . . . . . . . . . . . 145 Color-space formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146 Complementing color-space data . . . . . . . . . . . . . . . . . . . . . . . . . 147 2-base encoding and error recognition . . . . . . . . . . . . . . . . . . . . . 148 Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 Data analysis considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151 Understand Ns and color-space . . . . . . . . . . . . . . . . . . . . . . . . . . 151 Find Single Nucleotide Polymorphisms (SNPs) . . . . . . . . . . . . . . . 151 Color-space rules for SNP detection . . . . . . . . . . . . . . . . . . . . . . . 151 SNPs and errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 High accuracy for SNP detection . . . . . . . . . . . . . . . . . . . . . . . . . . 153 SNP error rates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154 Sampling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 Allele ratio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 Find polymorphisms in color-space . . . . . . . . . . . . . . . . . . . . . . . . 155 Appendix C Advanced Topic: Data Management . . . . . . . . . . . . 157 Saving data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 Approximate storage space for all data . . . . . . . . . . . . . . . . . . . . . 157 Raw image data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158 Primary analysis results data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158 Data transfer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160 Exporting data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160 Appendix D Advanced Topic: Primary Analysis . . . . . . . . . . . . . . 161 What is primary analysis? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 Primary analysis overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162 Primary analysis workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 Primary analysis inputs and outputs . . . . . . . . . . . . . . . . . . . . . . . 165 Storage requirements for primary analysis . . . . . . . . . . . . . . . . . . . 169 Perform primary re-analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170 5
Page 1 and 2: Applied Biosystems SOLiD 4 System
Page 3: 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 and 24: Define primary analysis settings Ap
Page 25 and 26: Primary analysis parameters 5. Clic
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
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Filter Fasta fails Applied Biosyste
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View History View Run History in SE
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Applied Biosystems SOLiD 4 System
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System Logs Applied Biosystems SOLi
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4 �� SETS So
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Imaging Metrics Report Applied Bios
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Cycle Heat Map Report Select a heat
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Chapter 4 View Reports View overall
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Exposure Time Report Applied Biosys
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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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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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Page 151 and 152:
Data analysis considerations Unders
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SNPs and errors High accuracy for S
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Sampling Allele ratio Applied Biosy
Page 157 and 158:
C Saving data Applied Biosystems SO
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Page 161 and 162:
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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