- Page 1: ABI PRISM ® SeqScape ® Software V
- Page 5 and 6: Specifying the Analysis Settings .
- Page 7 and 8: Adding Specimens and Importing Data
- Page 9 and 10: Editing the Data . . . . . . . . .
- Page 11 and 12: Understanding the Autoanalysis Mana
- Page 13 and 14: Appendix G Software Warranty Comput
- Page 15 and 16: Preface How to Use This Guide Purpo
- Page 17 and 18: Conventions Used in This Guide Safe
- Page 19 and 20: How to Obtain Services and Support
- Page 21 and 22: Introduction to ABI PRISM SeqScape
- Page 23 and 24: For Users of Earlier Versions of Se
- Page 25 and 26: About SeqScape Software About SeqSc
- Page 27 and 28: About SeqScape Software How the Sof
- Page 29 and 30: Getting Started 2 2 This chapter co
- Page 31 and 32: Hardware and Software Requirements
- Page 33 and 34: SeqScape Software Versions SeqScape
- Page 35 and 36: Installing the Full Version for the
- Page 37 and 38: Removing SeqScape Software Removing
- Page 39 and 40: Starting SeqScape Software for the
- Page 41 and 42: Starting SeqScape Software for the
- Page 43 and 44: Starting SeqScape Software for the
- Page 45 and 46: Starting SeqScape Software for the
- Page 47 and 48: Starting SeqScape Software for the
- Page 49 and 50: New Users Logging In for the First
- Page 51 and 52: SeqScape Software Structure Project
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SeqScape Software Toolbar The secon
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Menus on the Main SeqScape Window C
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Creating Analysis Defaults and Disp
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Analysis Defaults Settings Analysis
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Creating Analysis Protocols 5. Sele
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Creating Analysis Protocols Specify
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Creating Analysis Protocols 2. Sele
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Creating Analysis Protocols 2. Ente
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Specifying the Analysis Settings If
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Specifying the Analysis Settings 4.
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Specifying the Analysis Settings 6.
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Specifying Display Settings To spec
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Specifying Display Settings 5. Sele
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Specifying Display Settings d. To d
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Creating a Reference Data Group 4 4
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Reference Data Group (RDG) Referenc
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Reference Data Group (RDG) Download
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Creating a New RDG Using the Wizard
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Creating a New RDG Using the Wizard
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Creating a New RDG Using the Wizard
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Creating a New RDG Using SeqScape M
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Defining Regions of Interest (ROI)
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Defining Regions of Interest (ROI)
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ROI Tab Descriptions Columns in the
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Creating a Library Setting Up Your
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Creating a Library 8. Select a laye
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Creating New Layers The Library Edi
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Creating New Layers Adding a Refere
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Declaring Variants into an RDG Decl
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Declaring Variants into an RDG 4. I
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Declaring Variants into an RDG 6. A
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Creating an RDG from Aligned Consen
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Creating an RDG from Aligned Consen
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Creating an RDG from Aligned Consen
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Creating an RDG from Aligned Consen
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Creating a Project Template 5 5 Thi
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Creating a Project Template Creatin
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Saving Project Components Saving Pr
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Creating and Analyzing a Project 6
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Workflow for This Chapter Before Yo
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Using the New Project Wizard to Cre
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Using the New Project Wizard to Cre
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Using the New Project Wizard to Cre
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Adding Specimens and Importing Data
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Adding Specimens and Importing Data
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Adding Specimens and Importing Data
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Adding Specimens and Importing Data
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Adding Specimens and Importing Data
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Analyzing the Data 5. Click OK. A n
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Reanalyzing a Project Using a Diffe
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Incorporating Variants into the Pro
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Incorporating Variants into the Pro
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Incorporating Variants into the Pro
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Incorporating Variants into the Pro
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Incorporating Variants into the Pro
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Viewing the Results 7 7 This chapte
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About the Project Data About the Pr
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Project Views Table 7-1 Project Vie
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Project Views Table 7-1 Project Vie
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Project Views Table 7-1 Project Vie
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Segment Views Segment Views There a
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Segment Views Table 7-2 Segment Vie
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Sample Views Sample Views The sampl
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Sample Views Table 7-4 Sample Views
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Sample Views Table 7-4 Sample Views
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Viewing Variants Method 2 1. Open t
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Viewing the Reports Viewing the Rep
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Viewing the Reports and Project Res
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Analysis QC Report Figure 7-3 Analy
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Mutations Report The Mutations repo
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AA Variants Report AA Variants Repo
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Sequence Confirmation Report Sequen
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Library Search Report Library Searc
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RDG Report RDG Report The report co
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Genotyping Report Genotyping Report
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Genotyping Report Figure 7-12 Genot
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Customizing the Reports 2. Select o
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Reanalyzing and Editing Data 8 8 Th
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About Analysis Parameters About Ana
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About Analysis Parameters Table 8-1
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Changing the Analysis Parameters in
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Changing the Analysis Parameters in
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Changing the Analysis Parameters in
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Editing the Data Editing the Data A
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Editing a Sample or a Consensus Seq
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Adjusting the Clear Range The three
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Adjusting the Clear Range Using the
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Editing Variants Method 2 To view a
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Exporting and Printing Data and Rep
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Exporting Data Files Exporting Data
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Exporting Data Files Exporting a Sp
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Exporting Data Files Exporting a Sa
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Exporting Reports Exporting a Repor
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Printing Data and Reports Printing
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Printing Data and Reports 3. Select
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Printing Data and Reports 4. Select
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Printing Data and Reports 6. Use th
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Printing Data and Reports Table 9-3
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Sample and Consensus Quality Values
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Sample Quality Values Sample Qualit
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Consensus Quality Values Consensus
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Displaying Quality Values Customizi
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Displaying Quality Values Displayin
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Cumulative Quality Value Scoring in
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Cumulative Quality Value Scoring in
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Automating Analysis 11 11 This chap
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Integrating SeqScape and Data Colle
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Before You Start Is SeqScape proper
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Launching Autoanalysis Manger Launc
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Creating Required Files in the Data
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Creating Required Files in the Data
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Creating Required Files in the Data
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Creating Required Files in the Data
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Creating Required Files in the Data
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Creating Required Files in the Data
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Creating Required Files in the Data
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Scheduling and Starting a Run 2. Cl
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Understanding the Autoanalysis Mana
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Understanding the Autoanalysis Mana
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Basecallers and DyeSet/Primer Files
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Definitions and Naming The DyeSet/P
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ABI PRISM SeqScape Software v2.1 Us
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ABI PRISM SeqScape Software v2.1 Us
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ABI PRISM SeqScape Software v2.1 Us
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ABI PRISM SeqScape Software v2.1 Us
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ABI PRISM SeqScape Software v2.1 Us
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ABI PRISM SeqScape Software v2.1 Us
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ABI PRISM SeqScape Software v2.1 Us
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Frequently Asked Questions B B This
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Training and Documentation FAQs Tra
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General SeqScape Software FAQs Gene
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General SeqScape Software FAQs Tabl
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SeqScape Manager FAQs SeqScape Mana
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SeqScape Manager FAQs Table B-5 Seq
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SeqScape Manager FAQs Table B-5 Seq
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Mutation, Variant, HIM, and HFM Det
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Data Analysis FAQs Table B-8 Data A
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Quality Values FAQs Table B-9 Analy
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Audit Trail, Security, and Access C
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Translation Tables C C This appendi
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IUPAC Diagrams IUPAC Diagrams IUPAC
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Amino Acid Abbreviations Amino Acid
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User Privileges D D Tables of User
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Tables of User Privileges Table D-2
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Tables of User Privileges Table D-3
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Tables of User Privileges Table D-3
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Tables of User Privileges Table D-3
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Aligned Variant and FASTA File Form
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FASTA File Format FASTA File Format
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FASTA File Format Table E-1 Accepte
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Creating a Multi-Aligned FASTA File
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Method 1: Create a Multi-Aligned FA
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Method 2: Create a Multi-Aligned FA
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Method 2: Create a Multi-Aligned FA
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Software Warranty G G Computer Conf
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Limited Product Warranty Warranty L
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Glossary ABI basecaller administrat
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DyeSet/Primer file export FASTA for
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Sample Manager sample quality value
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Index Numerics 310 Basecaller and D
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creating a library 4-20 an RDG, abo
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learning software, wizard 4-6 libra
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S sample bases, editing 8-14 data,
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Headquarters 850 Lincoln Centre Dri