SeqScape Software Version 2.1 User Guide - InfoNet

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Preparing to Install SeqScape Software . . . . . . . . . . . . . . . . . . . . . . . 2-6 Installing the Full Version for the First Time . . . . . . . . . . . . . . . . . . . . . 2-7 Upgrading from SeqScape Software Versions 1.0, 1.1, or 2.0 . . . . . . 2-8 About the Upgrade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8 Upgrading to v2.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8 Existing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8 Removing SeqScape Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9 What the Uninstallation Process Does . . . . . . . . . . . . . . . . . . . . . 2-9 Removing the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9 Starting SeqScape Software for the First Time . . . . . . . . . . . . . . . . . 2-10 Before You Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10 File-Naming Convention . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10 Starting SeqScape Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11 Creating New Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13 Setting Up Authentication & Audit . . . . . . . . . . . . . . . . . . . . . . . . 2-15 Changing User Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-19 Setting Up the Default Directory . . . . . . . . . . . . . . . . . . . . . . . . . 2-20 New Users Logging In for the First Time . . . . . . . . . . . . . . . . . . . . . . 2-21 When New Users Log In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-21 SeqScape Software Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-22 SeqScape Manager Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-22 Project Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-23 SeqScape Software Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-24 Menus on the Main SeqScape Window . . . . . . . . . . . . . . . . . . . . . . . 2-26 Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-28 Chapter 3 Creating Analysis Defaults and Display Settings Workflow for This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2 Analysis Defaults Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3 Creating Analysis Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3 Analysis Protocol Editor Tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4 Specifying the Basecall Settings . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4 Specifying the Mixed Bases Settings . . . . . . . . . . . . . . . . . . . . . . 3-7 Specifying Clear Range . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8 Specifying the Filter Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10 iv ABI PRISM SeqScape Software v2.1 User Guide DRAFT August 28, 2003 3:10 pm, SeqScapeUGTOC.fm
Specifying the Analysis Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-12 Gap and Extension Penalties . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-12 Setting Analysis Defaults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-14 Selecting the Analysis Default Settings for Individual Samples . . 3-17 Specifying Display Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18 Chapter 4 Creating a Reference Data Group Workflow for This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2 Reference Data Group (RDG) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3 About the Reference Data Group . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3 GenBank Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4 Downloading a GenBank File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5 About Creating a New Reference Data Group (RDG)s . . . . . . . . . . 4-5 Creating a New RDG Using the Wizard . . . . . . . . . . . . . . . . . . . . . . . . 4-6 Using the Wizard to Learn the Software . . . . . . . . . . . . . . . . . . . . . 4-6 Setting Up the Reference Segment . . . . . . . . . . . . . . . . . . . . . . . 4-10 Creating a New RDG Using SeqScape Manager . . . . . . . . . . . . . . . . 4-12 Before You Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-12 Creating an RDG from SeqScape Manager . . . . . . . . . . . . . . . . . 4-12 About the Reference Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . 4-12 Importing a Reference Segment . . . . . . . . . . . . . . . . . . . . . . . . . . 4-13 Defining Regions of Interest (ROI) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-15 Defining an ROI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-15 Pasting a Reference Segment . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-15 Deleting an ROI or Layer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-16 Deleting a Reference Segment . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-16 ROI Tab Descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-18 Layer Pane Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-18 The ROI Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-18 Columns in the ROI Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-19 Creating a Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-20 About the Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-20 Using Aligned FASTA Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-20 Using a Tool to Align the Files . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-20 Setting Up Your Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-21 Creating New Layers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-24 Adding a Reference Break in a Sequence . . . . . . . . . . . . . . . . . . 4-27 ABI PRISM SeqScape Software v2.1 User Guide DRAFT August 28, 2003 3:10 pm, SeqScapeUGTOC.fm v
Page 1 and 2: ABI PRISM ® SeqScape ® Software V
Page 3: Contents Preface How to Use This Gu
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 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
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 89 and 90:
Page 91 and 92:
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
Page 105 and 106:
Creating New Layers The Library Edi
Page 107 and 108:
Creating New Layers Adding a Refere
Page 109 and 110:
Declaring Variants into an RDG Decl
Page 111 and 112:
Declaring Variants into an RDG 4. I
Page 113 and 114:
Declaring Variants into an RDG 6. A
Page 115 and 116:
Creating an RDG from Aligned Consen
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Page 119 and 120:
Page 121 and 122:
Page 123 and 124:
Creating a Project Template 5 5 Thi
Page 125 and 126:
Creating a Project Template Creatin
Page 127 and 128:
Saving Project Components Saving Pr
Page 129 and 130:
Creating and Analyzing a Project 6
Page 131 and 132:
Workflow for This Chapter Before Yo
Page 133 and 134:
Using the New Project Wizard to Cre
Page 135 and 136:
Page 137 and 138:
Page 139 and 140:
Adding Specimens and Importing Data
Page 141 and 142:
Page 143 and 144:
Page 145 and 146:
Page 147 and 148:
Page 149 and 150:
Analyzing the Data 5. Click OK. A n
Page 151 and 152:
Reanalyzing a Project Using a Diffe
Page 153 and 154:
Incorporating Variants into the Pro
Page 155 and 156:
Page 157 and 158:
Page 159 and 160:
Page 161 and 162:
Page 163 and 164:
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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Page 171 and 172:
Page 173 and 174:
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
Page 185 and 186:
Viewing the Reports Viewing the Rep
Page 187 and 188:
Viewing the Reports and Project Res
Page 189 and 190:
Analysis QC Report Figure 7-3 Analy
Page 191 and 192:
Mutations Report The Mutations repo
Page 193 and 194:
AA Variants Report AA Variants Repo
Page 195 and 196:
Sequence Confirmation Report Sequen
Page 197 and 198:
Library Search Report Library Searc
Page 199 and 200:
RDG Report RDG Report The report co
Page 201 and 202:
Genotyping Report Genotyping Report
Page 203 and 204:
Genotyping Report Figure 7-12 Genot
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Customizing the Reports 2. Select o
Page 207 and 208:
Reanalyzing and Editing Data 8 8 Th
Page 209 and 210:
About Analysis Parameters About Ana
Page 211 and 212:
About Analysis Parameters Table 8-1
Page 213 and 214:
Changing the Analysis Parameters in
Page 215 and 216:
Page 217 and 218:
Page 219 and 220:
Editing the Data Editing the Data A
Page 221 and 222:
Editing a Sample or a Consensus Seq
Page 223 and 224:
Adjusting the Clear Range The three
Page 225 and 226:
Adjusting the Clear Range Using the
Page 227 and 228:
Editing Variants Method 2 To view a
Page 229 and 230:
Exporting and Printing Data and Rep
Page 231 and 232:
Exporting Data Files Exporting Data
Page 233 and 234:
Exporting Data Files Exporting a Sp
Page 235 and 236:
Exporting Data Files Exporting a Sa
Page 237 and 238:
Exporting Reports Exporting a Repor
Page 239 and 240:
Printing Data and Reports Printing
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Printing Data and Reports 3. Select
Page 243 and 244:
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
Page 251 and 252:
Sample Quality Values Sample Qualit
Page 253 and 254:
Consensus Quality Values Consensus
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Displaying Quality Values Customizi
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Displaying Quality Values Displayin
Page 259 and 260:
Cumulative Quality Value Scoring in
Page 261 and 262:
Cumulative Quality Value Scoring in
Page 263 and 264:
Automating Analysis 11 11 This chap
Page 265 and 266:
Integrating SeqScape and Data Colle
Page 267 and 268:
Before You Start Is SeqScape proper
Page 269 and 270:
Launching Autoanalysis Manger Launc
Page 271 and 272:
Creating Required Files in the Data
Page 273 and 274:
Page 275 and 276:
Page 277 and 278:
Page 279 and 280:
Page 281 and 282:
Page 283 and 284:
Page 285 and 286:
Scheduling and Starting a Run 2. Cl
Page 287 and 288:
Understanding the Autoanalysis Mana
Page 289 and 290:
Understanding the Autoanalysis Mana
Page 291 and 292:
Basecallers and DyeSet/Primer Files
Page 293 and 294:
Definitions and Naming The DyeSet/P
Page 295 and 296:
ABI PRISM SeqScape Software v2.1 Us
Page 297 and 298:
Page 299 and 300:
Page 301 and 302:
Page 303 and 304:
Page 305 and 306:
Page 307 and 308:
Page 309 and 310:
Frequently Asked Questions B B This
Page 311 and 312:
Training and Documentation FAQs Tra
Page 313 and 314:
General SeqScape Software FAQs Gene
Page 315 and 316:
General SeqScape Software FAQs Tabl
Page 317 and 318:
SeqScape Manager FAQs SeqScape Mana
Page 319 and 320:
SeqScape Manager FAQs Table B-5 Seq
Page 321 and 322:
SeqScape Manager FAQs Table B-5 Seq
Page 323 and 324:
Mutation, Variant, HIM, and HFM Det
Page 325 and 326:
Data Analysis FAQs Table B-8 Data A
Page 327 and 328:
Quality Values FAQs Table B-9 Analy
Page 329 and 330:
Audit Trail, Security, and Access C
Page 331 and 332:
Translation Tables C C This appendi
Page 333 and 334:
IUPAC Diagrams IUPAC Diagrams IUPAC
Page 335 and 336:
Amino Acid Abbreviations Amino Acid
Page 337 and 338:
User Privileges D D Tables of User
Page 339 and 340:
Tables of User Privileges Table D-2
Page 341 and 342:
Page 343 and 344:
Page 345 and 346:
Page 347 and 348:
Aligned Variant and FASTA File Form
Page 349 and 350:
FASTA File Format FASTA File Format
Page 351 and 352:
FASTA File Format Table E-1 Accepte
Page 353 and 354:
Creating a Multi-Aligned FASTA File
Page 355 and 356:
Method 1: Create a Multi-Aligned FA
Page 357 and 358:
Page 359 and 360:
Page 361 and 362:
Software Warranty G G Computer Conf
Page 363 and 364:
Limited Product Warranty Warranty L
Page 365 and 366:
Glossary ABI basecaller administrat
Page 367 and 368:
DyeSet/Primer file export FASTA for
Page 369 and 370:
Sample Manager sample quality value
Page 371 and 372:
Index Numerics 310 Basecaller and D
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creating a library 4-20 an RDG, abo
Page 375 and 376:
learning software, wizard 4-6 libra
Page 377 and 378:
S sample bases, editing 8-14 data,
Page 380:
Headquarters 850 Lincoln Centre Dri
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