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

More documents

Recommendations

Info

4 Chapter 4 View Reports View overall run reports Bead definitions Bead Type Definition Usable Beads Beads that, in a particular ligation cycle, are mapped in each of the four images. Typically, most beads in a panel are usable. The ones that are not lie near the edge of the panel, which for current purposes is defined as the area imaged by the corresponding reference or focal map image. The ligation fluorescence images must be shifted a few to tens of pixels to register them with the reference image. If, for example, a ligation image must be shifted 10 pixels to the left to register with the reference image, beads within 10 pixels of the right edge of the panel will not be mapped in that ligation image. Another common case is a panel-cycle where one of the ligation images fails to register. In this case, none of the beads are usable. Good Beads Usable beads that satisfy all of the following conditions: intensity >0.05 0.0125 < angle ≤0.05 Best Beads Usable beads that satisfy all of the following conditions: intensity >0.05 angle ≤0.0125 68 Applied Biosystems SOLiD 4 System SETS Software User Guide
Chapter 4 View Reports View overall run reports 4 Cycle Scans view Use the Cycle Scans window to distinguish normal runs from problematic runs. Click Cycle Scans (Run Details�Overall Reports). The top section of the Cycle Scans window lists all the scans per ligation cycle for the slide, and the bottom section shows scan information sorted by sample for the scan selected in the top section. Use the parameters shown in the table on the next page to assess the progress of the sequencing run. See “View Cycle Scans” on page 46 for more details. Applied Biosystems SOLiD 4 System SETS Software User Guide 69
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:
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 39 and 40: Applied Biosystems SOLiD 4 System
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 59 and 60: Applied Biosystems SOLiD 4 System
Page 61 and 62: System Logs Applied Biosystems SOLi
Page 65 and 66: Imaging Metrics Report Applied Bios
Page 67: Cycle Heat Map Report Select a heat
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 ...

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?