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

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6 Chapter 6 Support Multiplexing Multiplexing Assignment Report Import a Multiplexing Series The Multiplexing Assignment report shows the number of barcode reads assigned to each library, along with the subtotals for all libraries. It also shows the number of reads that were not assigned to any specified library. These numbers include both passed and failed reads from the filter fasta stage. The value in the “0 Mismatch” column is the number of barcode reads that match exactly to the barcode shown in the barcode column. The “1 Mismatch” column is the number that missed matching that barcode by one. Reads that did not match any of the barcodes at the specified level are counted in the unassigned library with the name unresolved. It is possible that barcodes in the kit that were not assigned to a library are also matched. In that case, the unassigned library may show barcodes named with the color sequence of the matched barcode. Two additional libraries may appear: For beads that have barcode read but no F3 read (missing-f3). For reads that have an F3 read but no barcode read 9missingbc). The “Total % Assigned” is the sum of the library subtotals divided by the “All Beads Total” expressed as a percent. Follow the steps that use the Command line to import a multiplexing series found in the Applied Biosystems SOLiD 4 System ICS Software Help. Multiplexing report Multiplexing report can be attained as soon as barcoding is complete for a run. 110 Applied Biosystems SOLiD 4 System SETS Software User Guide
Reassign Run Applied Biosystems SOLiD 4 System SETS Software User Guide Chapter 6 Support Multiplexing Reassign Run 6 1. Download the sample sheet of the run that you want to reassign. 2. Open the sample sheet in excel and edit the barcoding reassignment or spot reassignment. Note: When reassigning the spots, ensure that the new, or edited, sample sheet has the same number of spots. 3. Log in as Administrator. 4. From Home page, click Reassign Run. 5. Click Log on�enter your name�enter password. 6. From the Home page, click on the analyses result of your choice, then click Reassign Run. Importing a new run definition for an existing run will force regeneration of all results. 111
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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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Page 61 and 62: System Logs Applied Biosystems SOLi
Page 63 and 64: 4 �� SETS So
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
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: Multiplexing Assignment report Appl
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
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
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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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