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

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D Appendix D Advanced Topic: Primary Analysis Primary analysis workflow images.dir.4=Solid_20080310_1/Solid_20080310_1_F3_P2_01_ V1 images.dir.5=Solid_20080310_1/Solid_20080310_1_F3_P1_01_ V1 images.dir.6=Solid_20080310_1/Solid_20080310_1_F3_P5_02_ V1 images.dir.7=Solid_20080310_1/Solid_20080310_1_F3_P4_02_ V1 images.dir.8=Solid_20080310_1/Solid_20080310_1_F3_P3_02_ V1 images.dir.9=Solid_20080310_1/Solid_20080310_1_F3_P2_02_ V1 images.dir.10=Solid_20080310_1/Solid_20080310_1_F3_P1_02 _V1 images.dir.11=Solid_20080310_1/Solid_20080310_1_F3_P5_03 _V1 images.dir.12=Solid_20080310_1/Solid_20080310_1_F3_P4_03 _V1 images.dir.13=Solid_20080310_1/Solid_20080310_1_F3_P3_03 _V1 images.dir.14=Solid_20080310_1/Solid_20080310_1_F3_P2_03 _V1 images.dir.15=Solid_20080310_1/Solid_20080310_1_F3_P1_03 _V1 images.dir.16=Solid_20080310_1/Solid_20080310_1_F3_P5_04 _V1 images.dir.17=Solid_20080310_1/Solid_20080310_1_F3_P4_04 _V1 images.dir.18=Solid_20080310_1/Solid_20080310_1_F3_P3_04 _V1 images.dir.19=Solid_20080310_1/Solid_20080310_1_F3_P2_04 _V1 images.dir.20=Solid_20080310_1/Solid_20080310_1_F3_P1_04 _V1 images.dir.21=Solid_20080310_1/Solid_20080310_1_F3_P5_05 _V1 172 Applied Biosystems SOLiD 4 System SETS Software User Guide
Appendix D Advanced Topic: Primary Analysis Primary analysis workflow D images.dir.22=Solid_20080310_1/Solid_20080310_1_F3_P4_05 _V1 images.dir.23=Solid_20080310_1/Solid_20080310_1_F3_P3_05 _V1 images.dir.24=Solid_20080310_1/Solid_20080310_1_F3_P2_05 _V1 images.dir.25=Solid_20080310_1/Solid_20080310_1_F3_P1_05 _V1 images.dir.26=Solid_20080310_1/Solid_20080310_1_F3_P5_06 _V1 images.dir.27=Solid_20080310_1/Solid_20080310_1_F3_P4_06 _V1 images.dir.28=Solid_20080310_1/Solid_20080310_1_F3_P3_06 _V1 images.dir.29=Solid_20080310_1/Solid_20080310_1_F3_P2_06 _V1 images.dir.30=Solid_20080310_1/Solid_20080310_1_F3_P1_06 _V1 images.dir.31=Solid_20080310_1/Solid_20080310_1_F3_P5_07 _V1 images.dir.32=Solid_20080310_1/Solid_20080310_1_F3_P4_07 _V1 images.dir.33=Solid_20080310_1/Solid_20080310_1_F3_P3_07 _V1 images.dir.34=Solid_20080310_1/Solid_20080310_1_F3_P2_07 _V1 images.dir.35=Solid_20080310_1/Solid_20080310_1_F3_P1_07 _V1 ################################# ##- Daemon Properties ##- These are optional ##- analysis.ini=/data/results/Solid/Solid_20080310_1/DH10B/ jobs/postPrimerSetPrimary.m1/PrimaryParameters.ini analysis.name=Filter_Fasta Applied Biosystems SOLiD 4 System SETS Software User Guide 173
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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
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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
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 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 171: Appendix D Advanced Topic: Primary
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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