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

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B Appendix B Advanced Topic: Data Analysis Overview Fundamentals of color-space analysis The primer is periodically reset for five or more independent rounds of extension reactions, improving the signal-to-noise ratio of the system. Each base is interrogated twice in two independent primer rounds, increasing confidence in each call. Four dyes are used to encode for sixteen possible 2-base combinations. The design of the encoding matrix enables builtin error-checking capability. 144 Applied Biosystems SOLiD 4 System SETS Software User Guide
Appendix B Advanced Topic: Data Analysis Overview Color-space and base space as applied in the SOLiD 4 System B Color-space and base space as applied in the SOLiD 4 System Color-space data The final files generated by the SOLiD 4 System are in base space. To maximize the built-in error correction of 2-base encoding, all file analysis is conducted in color-space prior to final results. Rather than reading one base per cycle, the software measures information on two bases simultaneously. In each cycle, the software calls one of four colors (color-space call). Because each ligation measurement event measures two bases, all bases (except for the final base of a read) are interrogated twice, providing for an additional level of error correction. Relationship between cycle and base position Figure 4 shows the relationship between color-space, base position, and the sequencing chemistry. Base number refers to base position. Base 0 is the last base of the adapter and is not part of the target sequence. The five primer lines show the order in which the data was generated (0-indexed). Note: In all files, only processed data refers to a color-space position. Applied Biosystems SOLiD 4 System SETS Software User Guide 145
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Applied Biosystems SOLiD 4 System
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How to use this guide Applied Biosy
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1 �� SETS So
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Naming convention for sequencing re
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SETS homepage Applied Biosystems SO
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2 �� SETS So
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SOLiD 4 System Software workflow A
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Log in to SETS Applied Biosystems S
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Define primary analysis settings Ap
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Primary analysis parameters 5. Clic
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Parameter Description Applied Biosy
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Parameter Description Applied Biosy
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Parameter Description Application D
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Define secondary analysis settings
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Chapter 2 Prepare Run Settings Set
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Load a Reference Sequence Specify a
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3 �� SETS So
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Note: For in-progress runs, you can
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Note: Refer to the Imaging Metrics
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Chapter 3 Monitor the Run in SETS V
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View sample data Applied Biosystems
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Troubleshoot failed jobs Sample ana
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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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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
Page 93 and 94: Master Report Tool Generate a Maste
Page 95 and 96: Chapter 4 View Reports Master Repor
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Page 99 and 100: Chapter 5 Perform Reanalysis Primar
Page 101 and 102: Effect on the current run Applied B
Page 105 and 106: View Multiplexing Series in SETS Ac
Page 107 and 108: Set up Multiplexing run in ICS Crea
Page 109 and 110: Multiplexing Assignment report Appl
Page 111 and 112: Reassign Run Applied Biosystems SOL
Page 115 and 116: Auto export in SETS Applied Biosyst
Page 117 and 118: Auto export with JMS broker and Exp
Page 119 and 120: 3. Run the following command: Appli
Page 121 and 122: Manually configure the RSA keys App
Page 123 and 124: Change export for current run only
Page 125 and 126: Event notifications and email servi
Page 127 and 128: Applied Biosystems SOLiD 4 System
Page 129 and 130: Delete runs Applied Biosystems SOLi
Page 131 and 132: Chapter 7 Manage Administrative Tas
Page 133 and 134: A Overview Applied Biosystems SOLiD
Page 135 and 136: Appendix A Web Services WSDL A Bind
Page 137 and 138: B Applied Biosystems SOLiD 4 Syste
Page 139 and 140: Appendix B Advanced Topic: Data Ana
Page 143: Applied Biosystems SOLiD 4 System
Page 147 and 148: Complementing color-space data Appl
Page 151 and 152: Data analysis considerations Unders
Page 153 and 154: SNPs and errors High accuracy for S
Page 155 and 156: Sampling Allele ratio Applied Biosy
Page 157 and 158: C Saving data Applied Biosystems SO
Page 161 and 162: D What is primary analysis? Applied
Page 163 and 164: Primary analysis workflow Applied B
Page 165 and 166: Primary analysis inputs and outputs
Page 167 and 168: Appendix D Advanced Topic: Primary
Page 169 and 170: Storage requirements for primary an
Page 175 and 176: Redo the read-filtering process App
Page 177 and 178: Image metrics Applied Biosystems SO
Page 181 and 182: Usage Validation and observed quali
Page 183 and 184: Key files generated by primary anal
Page 185 and 186: .spch files Applied Biosystems SOLi
Page 187 and 188: Troubleshooting analysis failure Ap
Page 191 and 192: E Applied Biosystems SOLiD 4 Syste
Page 193 and 194: 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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