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

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4 Chapter 4 View Reports View overall run reports Parameter Normal Run Problematic Run Failed panels In general, the number of failed panels should be relatively small and consistent. Fraction of Best + Good beads/Usable beads Effective exposure times The fraction can vary depending on the quality of the library, the efficiency of the PCR, and the enrichment process. As a guideline, the fraction is around 0.5 to 0.6 in the first ligation cycle of each primer and drops to 0.2 to 0.3 in the last cycle. Gradual increase from ligation cycles 1 to 5 or higher for each sequence primer. Performance varies from slide to slide and as a function of the age of the SOLiD Light Source. As a guideline, the effective exposure time is typically 20 to 40 ms in the first ligation cycle and increases to 100 to 300 ms in the fifth cycle. Satay plots The first cycle of any primer should show a relatively “clean” Satay plot, with most points clustered on the four color axes and with minimal fraction of the points clustered around the origin. The quality of the Satay plot typically degrades gradually with each ligation cycle for a single primer cycle, becoming more “fuzzy” in the last cycle. Run begins with extremely high number of failed panels or dramatic increase in any subsequent ligation cycle for each sequencing primer. A significant drop in the fraction of good beads in the initial ligation cycles is a reason to pause the run and troubleshoot the performance. 250 ms or greater in ligation cycle 1 or when instrument times out when the effective exposure time exceeds 500 ms. Long exposure times may indicate replacement of the SOLiD Light Source. An abnormal “fuzzy” Satay plot in the first cycle is a reason to pause the run and troubleshoot the performance. 70 Applied Biosystems SOLiD 4 System SETS Software User Guide
Exposure Time Report Applied Biosystems SOLiD 4 System SETS Software User Guide Chapter 4 View Reports View overall run reports 4 The Exposure Time report displays the average exposure time of run cycle scans for each of the four channels (6-FAM , Cy3 ® , Texas Red ® , and Cy5 ® dyes). In this report, you can: Mouse over any data point to see the called value. Export the Average Exposure Time table in a CSV format. Click Exposure Time Report (Run Details�Overall Reports). 71
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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
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
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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
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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
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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: Chapter 4 View Reports View overall
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 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
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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
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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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