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

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2 Chapter 2 Prepare Run Settings Load a Reference Sequence 5. From the Home page, navigate to the Secondary Analysis Settings and click New. Ensure that the reference genome file (MY_REFERENCE.fasta) appears in the Reference genome drop-down list, as shown in the example below. 40 Applied Biosystems SOLiD 4 System SETS Software User Guide
3 �� SETS Software Overview �� Prepare Run Settings �� Monitor the Run in SETS �� View Reports �� Perform Reanalysis �� Support Multiplexing �� Manage Administrative Tasks This chapter covers: Applied Biosystems SOLiD 4 System SETS Software User Guide Chapter 3 Monitor the Run in SETS ■ Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 ■ View Run Metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 ■ View Cycle Scans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 ■ View sample data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 ■ Troubleshoot failed jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 ■ View History. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 ■ Cancel analysis midstream . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 ■ Cluster Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 ■ System Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 ■ RSS feed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 41
Page 1 and 2: Applied Biosystems SOLiD 4 System
Page 7 and 8: How to use this guide Applied Biosy
Page 9 and 10: 1 �� SETS So
Page 11 and 12: Naming convention for sequencing re
Page 13 and 14: SETS homepage Applied Biosystems SO
Page 19 and 20: SOLiD 4 System Software workflow A
Page 21 and 22: Log in to SETS Applied Biosystems S
Page 23 and 24: Define primary analysis settings Ap
Page 25 and 26: Primary analysis parameters 5. Clic
Page 27 and 28: Parameter Description Applied Biosy
Page 29 and 30: Parameter Description Applied Biosy
Page 31 and 32: Parameter Description Application D
Page 33 and 34: Define secondary analysis settings
Page 35 and 36: Chapter 2 Prepare Run Settings Set
Page 37 and 38: Load a Reference Sequence Specify a
Page 39: Applied Biosystems SOLiD 4 System
Page 43 and 44: Note: For in-progress runs, you can
Page 45 and 46: Note: Refer to the Imaging Metrics
Page 47 and 48: Chapter 3 Monitor the Run in SETS V
Page 49 and 50: View sample data Applied Biosystems
Page 51 and 52: Troubleshoot failed jobs Sample ana
Page 53 and 54: Colorcall Jobs Applied Biosystems S
Page 55 and 56: Filter Fasta fails Applied Biosyste
Page 57 and 58: View History View Run History in SE
Page 61 and 62: System Logs Applied Biosystems SOLi
Page 65 and 66: Imaging Metrics Report Applied Bios
Page 67 and 68: Cycle Heat Map Report Select a heat
Page 69 and 70: Chapter 4 View Reports View overall
Page 71 and 72: Exposure Time Report Applied Biosys
Page 73 and 74: Chapter 4 View Reports View overall
Page 75 and 76: Determine the optimal titration poi
Page 77 and 78: View sample reports Applied Biosyst
Page 79 and 80: Resizing images Applied Biosystems
Page 81 and 82: Scaled data Applied Biosystems SOLi
Page 83 and 84: Angle data Applied Biosystems SOLiD
Page 85 and 86: View Analysis Reports Applied Biosy
Page 87 and 88: View analysis Data Files View Analy
Page 89 and 90: 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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Applied Biosystems SOLiD 4 System
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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
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Appendix B Advanced Topic: Data Ana
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Appendix B Advanced Topic: Data Ana
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Complementing color-space data Appl
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Data analysis considerations Unders
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SNPs and errors High accuracy for S
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Sampling Allele ratio Applied Biosy
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C Saving data Applied Biosystems SO
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D What is primary analysis? Applied
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Primary analysis workflow Applied B
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Primary analysis inputs and outputs
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Appendix D Advanced Topic: Primary
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Storage requirements for primary an
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Redo the read-filtering process App
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Image metrics Applied Biosystems SO
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Usage Validation and observed quali
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Key files generated by primary anal
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.spch files Applied Biosystems SOLi
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Troubleshooting analysis failure Ap
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E Applied Biosystems SOLiD 4 Syste
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LICENSE Appendix E Software License
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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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