SeqScape Software Version 2.1 User Guide - InfoNet

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Chapter 2 Getting Started SeqScape Software Structure SeqScape software is organized around two main windows: • SeqScape Manager window, from which you enter and manage the information necessary to perform analyses • Project window, from which you manage the results of analyses SeqScape v2.1 Software Main Window SeqScape Manager Project Window Projects Project Template Project View Report Manager Analysis QC Report Sample Manager Sample Parameters Reference Data Group Analysis Protocols Analysis Defaults Display Settings Libraries Specimen View Segment View Sample View Mutations Report AA Variants Report Specimen Statistics Report Sequence Confirmation Report Base Frequency Report Analysis Protocol Library Search Report RDG Report Audit Trail Report Genotyping Report Compare View and Edit Data View, Export, or Print Results Edit and Apply Figure 2-2 SeqScape Software Structure SeqScape Manager Window In the SeqScape Manager, you configure projects by creating project templates. The project templates can be reused in multiple projects and can be exported to be shared with other researchers. The project templates contain: • Reference sequence information • Analysis settings (including analysis protocols) • Display settings 2-22 ABI PRISM SeqScape Software v2.1 User Guide DRAFT August 28, 2003 2:54 pm, 2_Getting_Started.fm
SeqScape Software Structure Project Window In the Project window, you can view your data in the following ways: Table 2-3 Views in the Project Window View Project View Specimen View Segment View Sample View Description Shows the reference sequence, each specimen consensus sequence, and electropherogram snippets for each sample file in each specimen. The Expanded Nucleotide View shows all the nucleotides. The Collapsed Nucleotide View shows only variants of the nucleotides. The Expanded Amino Acid View shows all the amino acids. Characters (NT or AA) that are the same as the reference are shown as dots. The Character/Dots button switches to show or hide the view. The Identification pane, which shows the library search results, appears at the bottom of the Project view. Shows the clear range and orientation of each sample and how they line up to the reference sequence, and the overview pane with active ROIs. A table of sample information. Clicking a row in the table shows the corresponding sample sequence below. The Layout tab shows the direction of each sample within the segment. The Assembly tab shows samples aligned to the consensus sequence. An overview pane that represents forward and reverse sequences, variants, and ROIs. Electropherograms can be displayed for one or all sequences. Shows pertinent information for the sample, which includes annotation, sequence, electropherogram and raw data. Refer to Chapter 10, “Sample and Consensus Quality Values,” for detailed descriptions of these views. ABI PRISM SeqScape Software v2.1 User Guide 2-23 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 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 49: New Users Logging In for the First
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
Page 83 and 84: Reference Data Group (RDG) Referenc
Page 85 and 86: Reference Data Group (RDG) Download
Page 87 and 88: Creating a New RDG Using the Wizard
Page 93 and 94: Creating a New RDG Using SeqScape M
Page 95 and 96: Defining Regions of Interest (ROI)
Page 97 and 98: Defining Regions of Interest (ROI)
Page 99 and 100: ROI Tab Descriptions Columns in the
Page 101 and 102:
Creating a Library Setting Up Your
Page 103 and 104:
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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