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

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1 Chapter 1 SETS Software Overview SOLiD 4 System overview SOLiD 4 System overview SOLiD system technology IMPORTANT! The features presented in this document are related to the SOLiD 4 System SETS v4.0.1. The Applied Biosystems SOLiD 4 System provides parallel sequencing of clonally amplified DNA fragments linked to magnetic beads. The sequencing methodology is based on sequential ligation with dye-labeled oligonucleotides. All fluorescently labeled oligonucleotide probes are present simultaneously, competing for incorporation. After each ligation, fluorescence is measured before another round of ligation takes place. This ligation-based chemistry eliminates dephasing. The use of a two-base encoding mechanism, which interrogates each base twice for errors during sequencing, discriminates between true polymorphisms and system noise. The SOLiD 4 System software allows customers to monitor runs in real-time, and provides basic data analysis tools. The SOLiD 4 System consists of: SOLiD 4 Analyzer All ancillary equipment ICS software, which is described in the Applied Biosystems SOLiD 4 System ICS Software Help SOLiD Experiment Tracking System (SETS) software, which is described in this document 10 Applied Biosystems SOLiD 4 System SETS Software User Guide
Naming convention for sequencing reads Applied Biosystems SOLiD 4 System SETS Software User Guide Chapter 1 SETS Software Overview SOLiD 4 System overview 1 The following shows the naming convention for the sequencing runs. Fragment Paired-end Mate-pair Multiplex fragment Multiplex paired-end WFA (not shown below) Selecting a Fragment run and then selecting Multiplexing will result in creating a barcoded fragment library. The same concept applies to the Paired-End run. 11
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Page 7 and 8: How to use this guide Applied Biosy
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Page 13 and 14: SETS homepage Applied Biosystems SO
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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
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Page 43 and 44: Note: For in-progress runs, you can
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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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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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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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Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

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