Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

More documents

Recommendations

Info

4 Chapter 4 View Reports View overall run reports View overall run reports You can view information about a completed run by opening one of the overall run reports: Imaging Metrics Heat Map Report Cycle Heat Map Report Cycle Scans (View) Exposure Time Flowcell Mask WFA Report (will display only when applicable) Note: Most reports can be viewed in both real-time and completed run data. 64 Applied Biosystems SOLiD 4 System SETS Software User Guide
Imaging Metrics Report Applied Biosystems SOLiD 4 System SETS Software User Guide Chapter 4 View Reports View overall run reports 4 The Imaging Metrics report displays the cycle scan heat map view for all four channels (FAM , CY3 ® , Texas Red ® , and CY5 ® dyes) for the selected metric type, (for example, exposure). Definitions of all the metric types can be found in “Primary analysis parameters” on page 25. Click Imaging Metrics Report (Run Details�Overall Reports). 65
Page 1 and 2:
Applied Biosystems SOLiD 4 System
Page 3 and 4:
Page 5 and 6:
Page 7 and 8:
How to use this guide Applied Biosy
Page 9 and 10:
1 �� SETS So
Page 11 and 12:
Naming convention for sequencing re
Page 13 and 14: SETS homepage Applied Biosystems SO
Page 15 and 16: Applied Biosystems SOLiD 4 System
Page 17 and 18: 2 �� SETS So
Page 19 and 20: SOLiD 4 System Software workflow A
Page 21 and 22: Log in to SETS Applied Biosystems S
Page 23 and 24: Define primary analysis settings Ap
Page 25 and 26: Primary analysis parameters 5. Clic
Page 27 and 28: Parameter Description Applied Biosy
Page 29 and 30: Parameter Description Applied Biosy
Page 31 and 32: Parameter Description Application D
Page 33 and 34: Define secondary analysis settings
Page 35 and 36: Chapter 2 Prepare Run Settings Set
Page 37 and 38: Load a Reference Sequence Specify a
Page 43 and 44: Note: For in-progress runs, you can
Page 45 and 46: Note: Refer to the Imaging Metrics
Page 47 and 48: Chapter 3 Monitor the Run in SETS V
Page 49 and 50: View sample data Applied Biosystems
Page 51 and 52: Troubleshoot failed jobs Sample ana
Page 53 and 54: Colorcall Jobs Applied Biosystems S
Page 55 and 56: Filter Fasta fails Applied Biosyste
Page 57 and 58: View History View Run History in SE
Page 61 and 62: System Logs Applied Biosystems SOLi
Page 63: 4 �� SETS So
Page 67 and 68: Cycle Heat Map Report Select a heat
Page 69 and 70: Chapter 4 View Reports View overall
Page 71 and 72: Exposure Time Report Applied Biosys
Page 73 and 74: Chapter 4 View Reports View overall
Page 75 and 76: Determine the optimal titration poi
Page 77 and 78: View sample reports Applied Biosyst
Page 79 and 80: Resizing images Applied Biosystems
Page 81 and 82: Scaled data Applied Biosystems SOLi
Page 83 and 84: Angle data Applied Biosystems SOLiD
Page 85 and 86: View Analysis Reports Applied Biosy
Page 87 and 88: View analysis Data Files View Analy
Page 89 and 90: Auto-Correlation Report Applied Bio
Page 91 and 92: Error Profiles Report Applied Biosy
Page 93 and 94: Master Report Tool Generate a Maste
Page 95 and 96: Chapter 4 View Reports Master Repor
Page 99 and 100: Chapter 5 Perform Reanalysis Primar
Page 101 and 102: Effect on the current run Applied B
Page 105 and 106: View Multiplexing Series in SETS Ac
Page 107 and 108: Set up Multiplexing run in ICS Crea
Page 109 and 110: Multiplexing Assignment report Appl
Page 111 and 112: Reassign Run Applied Biosystems SOL
Page 115 and 116:
Auto export in SETS Applied Biosyst
Page 117 and 118:
Auto export with JMS broker and Exp
Page 119 and 120:
3. Run the following command: Appli
Page 121 and 122:
Manually configure the RSA keys App
Page 123 and 124:
Change export for current run only
Page 125 and 126:
Event notifications and email servi
Page 127 and 128:
Page 129 and 130:
Delete runs Applied Biosystems SOLi
Page 131 and 132:
Chapter 7 Manage Administrative Tas
Page 133 and 134:
A Overview Applied Biosystems SOLiD
Page 135 and 136:
Appendix A Web Services WSDL A Bind
Page 137 and 138:
B Applied Biosystems SOLiD 4 Syste
Page 139 and 140:
Appendix B Advanced Topic: Data Ana
Page 141 and 142:
Page 143 and 144:
Page 145 and 146:
Appendix B Advanced Topic: Data Ana
Page 147 and 148:
Complementing color-space data Appl
Page 149 and 150:
Page 151 and 152:
Data analysis considerations Unders
Page 153 and 154:
SNPs and errors High accuracy for S
Page 155 and 156:
Sampling Allele ratio Applied Biosy
Page 157 and 158:
C Saving data Applied Biosystems SO
Page 159 and 160:
Page 161 and 162:
D What is primary analysis? Applied
Page 163 and 164:
Primary analysis workflow Applied B
Page 165 and 166:
Primary analysis inputs and outputs
Page 167 and 168:
Appendix D Advanced Topic: Primary
Page 169 and 170:
Storage requirements for primary an
Page 171 and 172:
Page 173 and 174:
Page 175 and 176:
Redo the read-filtering process App
Page 177 and 178:
Image metrics Applied Biosystems SO
Page 179 and 180:
Page 181 and 182:
Usage Validation and observed quali
Page 183 and 184:
Key files generated by primary anal
Page 185 and 186:
.spch files Applied Biosystems SOLi
Page 187 and 188:
Troubleshooting analysis failure Ap
Page 189 and 190:
Page 191 and 192:
E Applied Biosystems SOLiD 4 Syste
Page 193 and 194:
LICENSE Appendix E Software License
Page 195 and 196:
Appendix E Software License Agreeme
Page 197 and 198:
Page 199 and 200:
Page 201 and 202:
Alignment Matrix The alignment matr
Page 203 and 204:
Page 205 and 206:
Glossary WFA A Workflow Analysis (W
Page 207 and 208:
Related documentation Document BioS
Page 209:
Part Number 4448411 Rev. B 04/2010
show all

Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

Create successful ePaper yourself

Delete template?

Save as template?