SeqScape Software Version 2.1 User Guide - InfoNet

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Chapter 2 Getting Started Hard Drive Partitions The installer uses the following location for SeqScape software files: drive letter:\Applied Biosystems\SeqScape The drive letter is determined by the following conditions: Table 2-2 Drive Letter Determination: If the computer … is not connected to a genetic analyzer has data collection software that is connected to a genetic analyzer The installer selects drive … D (default), or C (if D drive is not available) E 2-4 ABI PRISM SeqScape Software v2.1 User Guide DRAFT August 28, 2003 2:54 pm, 2_Getting_Started.fm
SeqScape Software Versions SeqScape Software Versions There are four versions of SeqScape Software v2.1 available: Software Version SeqScape Software v2.1 full release version SeqScape Software v2.1 upgrade SeqScape Software v2.1 update SeqScape Software v2.1 30-day demo Intended for a system that ... Has no SeqScape software installed, or has the 30-day demo version installed Has SeqScape software v1.0, 1.1, or 2.0 installed Has SeqScape v2.0 installed Meets the minimum requirements Existing Data Data created in v1.0, 1.1, or 2.0 will be moved to version 2.1. Data created in v1.0, 1.1, or 2.0 will be moved to version 2.1. Data created or saved in v2.0 will be moved to v2.1. IMPORTANT! This update does not work on systems with SeqScape software v1.0 or 1.1. You must export any files created in the 30- day demo version before the software expires. You can then import any exported files into the full release version of SeqScape v2.1. ABI PRISM SeqScape Software v2.1 User Guide 2-5 DRAFT August 28, 2003 2:54 pm, 2_Getting_Started.fm
Page 1 and 2: ABI PRISM ® SeqScape ® Software V
Page 3 and 4: Contents Preface How to Use This Gu
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: Hardware and Software Requirements
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 49 and 50: New Users Logging In for the First
Page 51 and 52: SeqScape Software Structure Project
Page 53 and 54: SeqScape Software Toolbar The secon
Page 55 and 56: Menus on the Main SeqScape Window C
Page 57 and 58: Creating Analysis Defaults and Disp
Page 59 and 60: Analysis Defaults Settings Analysis
Page 61 and 62: Creating Analysis Protocols 5. Sele
Page 63 and 64: Creating Analysis Protocols Specify
Page 65 and 66: Creating Analysis Protocols 2. Sele
Page 67 and 68: Creating Analysis Protocols 2. Ente
Page 69 and 70: Specifying the Analysis Settings If
Page 71 and 72: Specifying the Analysis Settings 4.
Page 73 and 74: Specifying the Analysis Settings 6.
Page 75 and 76: Specifying Display Settings To spec
Page 77 and 78: Specifying Display Settings 5. Sele
Page 79 and 80: Specifying Display Settings d. To d
Page 81 and 82: 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
Page 87 and 88:
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 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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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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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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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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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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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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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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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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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
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