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

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4 Chapter 4 View Reports View sample reports Color Balance Report Use this report to view the number of beads that have a particular color call for a specific ligation cycle. For most samples, the distribution of colors is relatively uniform across the four channels. However, a strong deviation from uniformity or an imbalance trend could indicate problems in the sequencing chemistry or imaging process, or a bias in the library preparation. In this report, you can: Mouse over any data point to see the called value. Export the Scan Bead Summary table to a CSV file. 84 Applied Biosystems SOLiD 4 System SETS Software User Guide
View Analysis Reports Applied Biosystems SOLiD 4 System SETS Software User Guide Chapter 4 View Reports View Analysis Reports 4 View sample files Auto-analysis creates fasta files and various report graphs from the analyzed sample data. Primer sets F3 and R3 are represented by links to csfasta files for F3 and R3. Note: When the analysis is successful for F3 and R3 primer sets, a csfasta file is generated. The “.csfasta” format is a text-based format that displays the base-pair sequences in color space (that is, bases display as 0, 1, 2, 3). Click each auto-analysis folder’s expansion arrow to see its contents. 85
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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
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
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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: Angle data Applied Biosystems SOLiD
Page 87 and 88: View analysis Data Files View Analy
Page 89 and 90: Auto-Correlation Report Applied Bio
Page 91 and 92: Error Profiles Report Applied Biosy
Page 93 and 94: Master Report Tool Generate a Maste
Page 95 and 96: Chapter 4 View Reports Master Repor
Page 99 and 100: Chapter 5 Perform Reanalysis Primar
Page 101 and 102: Effect on the current run Applied B
Page 105 and 106: View Multiplexing Series in SETS Ac
Page 107 and 108: Set up Multiplexing run in ICS Crea
Page 109 and 110: Multiplexing Assignment report Appl
Page 111 and 112: Reassign Run Applied Biosystems SOL
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 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
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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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