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

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D Appendix D Advanced Topic: Primary Analysis Procedures to verify primary analysis status Procedure for re-analyzing the image (primary analysis) If there was failure in the automatically-generated primary analysis pipeline, there are two ways to do primary re-analysis of the image. Before doing so, look at the primary log files to find out reason of failure. The log files are in the folder: /data/result/{instrument.name}/{run.name}/{sample.name}/ jobs/{stage.name}.[JobId]/analysis/ Also, ensure that all images are present at /data/images/{run.name}. After finding out the reason, change primary analysis parameters. To re-analyze through SETS: 1. Log in to SETS using an administrative account. 2. Modify the primary analysis settings. Either modify added parameters or add your new values in Additional parameter field. 3. Open the Run Details page for that run and do primary reanalysis. To perform primary analysis manually: 1. Access the job folder at: /data/result/{instrument.name}/{run.name}/{sample.n ame}/jobs/{stage.name}.[JobId]/ 2. Modify the parameters.ini file with the desired value. 3. Enter the following command: jprimaryanalysis.sh --dir= --ini= For example: jprimaryanalysis.sh -dir=/data/results/DAEMONAC2/LAST_MP_1245_041008/Sam ple1/jobs/ postPrimerSetPrimary.3793 -ini=parameters.ini 190 Applied Biosystems SOLiD 4 System SETS Software User Guide
E Applied Biosystems SOLiD 4 System SETS Software User Guide Appendix E Software License Agreement APPLIED BIOSYSTEMS END USER SOFTWARE LICENSE AGREEMENT FOR INSTRUMENT OPERATING AND ASSOCIATED BUNDLED SOFTWARE AND LIMITED PRODUCT WARRANTY Applied Biosystems SOLiD 4 System SETS Software NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY. THIS IS THE CONTRACT BETWEEN YOU AND LIFE TECHNOLOGIES REGARDING THE OPERATING SOFTWARE FOR YOUR APPLIED BIOSYSTEMS WORKSTATION OR OTHER INSTRUMENT AND BUNDLED SOFWARE INSTALLED WITH YOUR OPERATING SOFTWARE. THIS AGREEMENT CONTAINS WARRANTY AND LIABILITY DISCLAIMERS AND LIMITATIONS. YOUR INSTALLATION AND USE OF THE APPLIED BIOSYSTEMS SOFTWARE IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT. IF YOU DO NOT AGREE TO THE TERMS AND CONDITIONS OF THIS LICENSE, YOU SHOULD PROMPTLY RETURN THIS SOFTWARE, TOGETHER WITH ALL PACKAGING, TO APPLIED BIOSYSTEMS AND YOUR PURCHASE PRICE WILL BE REFUNDED. This Applied Biosystems End User License Agreement accompanies an Applied Biosystems software product (“Software”) and related explanatory materials (“Documentation”). The term “Software” also includes any upgrades, modified versions, updates, additions and copies of the Software licensed to you by Applied Biosystems. The 191
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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
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Manually configure the RSA keys App
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Change export for current run only
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Event notifications and email servi
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Delete runs Applied Biosystems SOLi
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Chapter 7 Manage Administrative Tas
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A Overview Applied Biosystems SOLiD
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Appendix A Web Services WSDL A Bind
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B Applied Biosystems SOLiD 4 Syste
Page 139 and 140: Appendix B Advanced Topic: Data Ana
Page 141 and 142: Applied Biosystems SOLiD 4 System
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 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 189: Applied Biosystems SOLiD 4 System
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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