SeqScape Software Version 2.1 User Guide - InfoNet

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Chapter 2 Getting Started 5. Enter your user name and password again, then click OK. The License dialog box opens. Figure 2-1 License Dialog 6. Read the license agreement then click Accept. 2-12 ABI PRISM SeqScape Software v2.1 User Guide DRAFT August 28, 2003 2:54 pm, 2_Getting_Started.fm
Starting SeqScape Software for the First Time The SeqScape software main window opens. Creating New Users Because SeqScape software tracks the projects and settings for each user, Applied Biosystems recommends that you create users for each individual who uses SeqScape software on the computer. The Users tab allows exporting of user names and access privileges for these users. IMPORTANT! The administrator is the only person who can set up and change the information in the Users tab. The selections in this tab are inactive for all other users. ABI PRISM SeqScape Software v2.1 User Guide 2-13 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: Starting SeqScape Software for the
Page 43 and 44: 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: Creating a New RDG Using the Wizard
Page 91 and 92:
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
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
Page 117 and 118:
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
Page 167 and 168:
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
Page 183 and 184:
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
Page 241 and 242:
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
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Consensus Quality Values Consensus
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Displaying Quality Values Customizi
Page 257 and 258:
Displaying Quality Values Displayin
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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
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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
Page 325 and 326:
Data Analysis FAQs Table B-8 Data A
Page 327 and 328:
Quality Values FAQs Table B-9 Analy
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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
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Amino Acid Abbreviations Amino Acid
Page 337 and 338:
User Privileges D D Tables of User
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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
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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
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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
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DyeSet/Primer file export FASTA for
Page 369 and 370:
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
Page 377 and 378:
S sample bases, editing 8-14 data,
Page 380:
Headquarters 850 Lincoln Centre Dri
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