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

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D Appendix D Advanced Topic: Primary Analysis Primary analysis workflow Perform primary re-analysis To perform primary analysis manually, use the following command: jprimaryanalysis.sh –-ini=PrimaryParametesr.ini Note: Only buildReads tasks are executed for re-analysis. Neither beadFinding nor colorCalling are enabled for re-analysis in the pipeline. The PrimaryParameters.ini file can be found inside the JobID folder with the file named parameters.ini. $sampleJobFolder/postPrimerSetPrimary To prepare for the re-analysis: 1. Create a new analysis directory, such as: postPrimerSetPrimary.m1. 2. Copy the following file onto the new directory. parameters.ini 3. Edit the following file to ensure that all the paths are correct. PrimaryParameters.ini 4. Remove parameters marked for daemon property. For example: analysis.job.id (Default behavior does not accept non-integer.) update.solid.script (Used by the daemon for updating the SOLiD 4 System database.) logging.socket (Used by the daemon for logging analysis progress.) 5. Enter jprimaryanalysis.sh --ini=PrimaryParameters.ini 170 Applied Biosystems SOLiD 4 System SETS Software User Guide
Appendix D Advanced Topic: Primary Analysis Primary analysis workflow D The following is an example of the PrimaryParameters.ini file: ###################################### ##- Primary Analysis Settings ##################################### ##- Instrument, sample, etc instrument.name=Solid run.name=Solid_20080310_1 sample.name=DH10B panels=1-2357 primer.set=F3 read.length=35 read.prefix=T ####################################### ##- Analysis Job Parameters focal.map.dir=Solid_20080310_1/Solid_20080310_1_FOCALMAP _V1 focal.map.stg=Solid_20080310_1/Solid_20080310_1_FOCALMAP _V1/Solid_20080310_1_FOCALMAP_V1.STG focal.map.version=1 ##- position map. Used for generating correct sequence order ##- images.dir.1=Solid_20080310_1/Solid_20080310_1_F3_P5_01_ V1 images.dir.2=Solid_20080310_1/Solid_20080310_1_F3_P4_01_ V1 images.dir.3=Solid_20080310_1/Solid_20080310_1_F3_P3_01_ V2 Applied Biosystems SOLiD 4 System SETS Software User Guide 171
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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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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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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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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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Chapter 5 Perform Reanalysis Primar
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Effect on the current run Applied B
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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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Auto export in SETS Applied Biosyst
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Auto export with JMS broker and Exp
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Page 121 and 122: Manually configure the RSA keys App
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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
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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
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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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