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

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D Appendix D Advanced Topic: Primary Analysis Primary analysis workflow Image analysis results ".spch" files (SOLiD Panel Cache HDF5) $sampleResultFolder/colorcalls/CACHE/{run.name}_[panelID ].spch (one full slide has 2357 panels) Satay “.png” files $sampleResultFolder/cycleplots Summary data $sampleResultFolder/colorcall_summary/{run.name}_FOCALMA P_V1.tab $sampleResultFolder/colorcall_summary/{run.name}_F3_P1_0 1_V1.tab .. $sampleResultFolder/colorcall_summary/{run.name}_R3_P1_0 1_V1.tab .. $sampleResultFolder/colorcall_summary/{run.name}_BC_P1_0 1_V1.tab Run status information (traffic light) $sampleResultFolder/traffic_lights/ Color-space F3 raw reads (.csfasta) $sampleResultFolder/primary.[17- digittimestamp]/reads/{run.name}_{sample.name}_F3.csfast a Color-space BC raw reads (.csfasta) $sampleResultFolder/primary.[17- digittimestamp]/reads/{run.name}_{sample.name}_BC.csfast a 166 Applied Biosystems SOLiD 4 System SETS Software User Guide
Appendix D Advanced Topic: Primary Analysis Primary analysis workflow D Color-space F3 raw reads for library (.csfasta) $sampleResultFolder/libraries/{library.name}/primary.[17 - digittimestamp1]/reads/{run.name}_{sample.name}_F3.csfas ta Color-space BC raw reads for library (.csfasta) $sampleResultFolder/libraries/{library.name}/primary.[17 - digittimestamp]/reads/{run.name}_{sample.name}_BC.csfast a F3 QV (.qual) file for library $sampleResultFolder//libraries/{library.name}/primary.[1 7- digittimestamp]/reads/{run.name}_{sample.name}_F3_QV.qua l BC QV (.qual) file for library $sampleResultFolder//libraries/{library.name}/primary.[1 7- digittimestamp]/reads/{run.name}_{sample.name}_BC_QV.qua l F3 Primary analysis statistics file (.stats) $sampleResultFolder/primary.[17- digittimestamp]/reads/{run.name}_{sample.name}_F3.stats BC Primary analysis statistics file (.stats) $sampleResultFolder/primary.[17- digittimestamp]/reads/{run.name}_{sample.name}_BC.stats F3 Primary analysis statistics file (.stats) for library $sampleResultFolder/libraries/{library.name}/primary.[17 - digittimestamp]/reads/{run.name}_{sample.name}_F3.stats Applied Biosystems SOLiD 4 System SETS Software User Guide 167
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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
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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
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 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: Primary analysis inputs and outputs
Page 169 and 170: Storage requirements for primary an
Page 171 and 172: Appendix D Advanced Topic: Primary
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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
Page 201 and 202: Alignment Matrix The alignment matr
Page 205 and 206: Glossary WFA A Workflow Analysis (W
Page 207 and 208: Related documentation Document BioS
Page 209: Part Number 4448411 Rev. B 04/2010
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