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

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B Appendix B Advanced Topic: Data Analysis Overview Color-space and base space as applied in the SOLiD 4 System b. Those mate-pairs where only one of the tags matched to the reference sequence (in color-space) are re-analyzed, and the non-matching tag is compared to the reference sequence. Because analysis can be constrained by the knowledge of the allowed distances, this process allows alignment with more disagreements and the use of a more CPU-intensive alignment algorithm. Note: Where possible, all data are presented in a fastacompatible format to facilitate use in a variety of applications. Final output files are in base space and relative to the submitted reference (for example, consensus file, variation file). 150 Applied Biosystems SOLiD 4 System SETS Software User Guide
Data analysis considerations Understand Ns and color-space Applied Biosystems SOLiD 4 System SETS Software User Guide Appendix B Advanced Topic: Data Analysis Overview Data analysis considerations B In the SOLiD 4 System, unknown color-space calls are represented as ‘.’ or N. By default, the system filters out bases with a single ‘.’ in the sequence and leaves only reads with color-space calls present at all positions. You can change this behavior by masking a specific position of a read. For example, if position 21 of a 35 bp run is missing color-space calls, you can mask this position. Find Single Nucleotide Polymorphisms (SNPs) SNPs are single base-pair mutations that usually consist of two alleles. Color-space rules allow the software to detect only valid SNP sites. According to the color-space rules, one isolated color change is always an error when you consider single nucleotide changes. Two adjacent color changes can be either an error or a valid SNP. To detect two adjacent SNPs, look for three adjacent color changes. There are very specific rules to determine which color changes are valid and which are not. Color-space rules for SNP detection In the simplest case, where you have a single base change, the following rules apply (Figure 6): For any given reference, there are only three valid double-color changes. For the other 12 possibilities, the 6 single-color and 6 two-color changes are invalid, since they would require multiple changes within that genomic region. For these complicated genomic changes, the software uses a more sophisticated algorithm. 151
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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
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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
Page 99 and 100: Chapter 5 Perform Reanalysis Primar
Page 101 and 102: Effect on the current run Applied B
Page 103 and 104: 6 �� SETS So
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 113 and 114: 7 �� SETS So
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 145 and 146: Appendix B Advanced Topic: Data Ana
Page 147 and 148: Complementing color-space data Appl
Page 149: Applied Biosystems SOLiD 4 System
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
Page 195 and 196: 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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