GeneMapper. Software Version 4.0 AFLP. System Analysis Getting Started Guide (PN )
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- みずき やまのかみしゃ
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1 GeneMapper v4.0 AFLP Getting Started Guide
2
3 GeneMapper v4.0 AFLP Getting Started Guide
4 Copyright 2005 Applied Biosystems Japan Ltd. All rights reserved. Applied Biosystems Applied Biosystems : Applera Corporation GeneMapper HID GeneMapper HID AFLP Keygene N.V : ABI PRISM Applied Biosystems GeneMapper SNaPshot AB Design Applera FAM GeneScan ROX SNPlex Applera Corporation AFLP Keygene N.V Apache Software Foundation ( Copyright The Apache Software Foundation.All rights reserved. ExoLab Project ( exolab.org/) Copyright 2000 Intalio Inc. All rights reserved. JNIRegistry is Copyright 1997 Timothy Gerard Endres, ICE Engineering, Inc., Windows Microsoft Corporation Oracle Oracle Corporation Applera Corporation is committed to providing the world s leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses. Part Number Rev. B 06/2005 ii GeneMapper Software Version 4.0 AFLP Getting Started Guide
5 v v vi vii 1 1 AFLP AFLP GeneMapper GeneMapper v Analysis Method Allele Peak Detector Peak Quality Quality Flags Size Quality #1: Analysis Method #2: #3: GeneMapper Software Version 4.0 AFLP Getting Started Guide iii
6 Genotypes Samples Plot Marker Bin Panel Bin Set Samples Genotypes iv GeneMapper Software Version 4.0 AFLP Getting Started Guide
7 GeneMapper AFLP (Amplified Fragment Length Polymorphisms) AFLP (Amplified Fragment Length Polymorphisms) Applied Biosystems GeneMapper Software Version 4.0 Installation and Administration Guide (PN ) GeneMapper v4.0 Microsoft Winows 0 [Enter] ( ) File Open Spot Set View Filter View All Applied Biosystems 2 GeneMapper Software Version 4.0 AFLP Getting Started Guide v
8 Control Console Oracle ID Sample Entry GeneMapper Software Version4.0 Installation and Administration Guide (PN ) GeneMapper Software Version 4.0 Installation and Administration Guide (PN ) GeneMapper Software Version 4.0 Installation and Administration Guide GeneMapper v4.0 GeneMapper Software Version 4.0 Getting Started Guides GeneMapper 5 Applied Biosystems Data Collection LOH AFLP SNaPshot SNPlex GeneMapper GeneMapper Software v4.0 Online Help GeneMapper [F1] Help Contents and IndexGeneMapper 3 GeneMapper Software Version 4.0 Quick Reference Guide GeneMapper GeneMapper Software Version 4.0 Reference and Troubleshooting Guide PDF GeneMapper Software Version 4.0 Documentation CD vii vi GeneMapper Software Version 4.0 AFLP Getting Started Guide
9 Applied Biosystems GeneMapper Help Contents and Index Customer Support FAQ Applied Biosystems MSDS Certification of Analysis PDF Applied Biosystems GeneMapper Software Version 4.0 AFLP Getting Started Guide vii
10 viii GeneMapper Software Version 4.0 AFLP Getting Started Guide
11 1 AFLP AFLP GeneMapper GeneMapper v GeneMapper Software Version 4.0 AFLP Getting Started Guide 1
12 1 AFLP AFLP AFLP AFLP (Amplified Fragment Length Polymorphism) DNA AFLP RFLP Restriction Fragment Length Polymorphism; PCR Polymerase Chain Reaction; DNA AFLP / 2 AFLP GeneMapper Applied Biosystems AFLP Applied Biosystems Applied Biosystems AFLP 1 5 Applied Biosystems DNA 2 EcoRI MseI Savelkoul, P. H. M., Aarts, H. J. M., de Haas, J., Dijkshoorn, L., Duim, B., Otsen, M., Rademaker, J. L. W., Schouls, L., and Lenstra, J. A., J Clin Microbio, 1999, 37(10), GeneMapper Software Version 4.0 AFLP Getting Started Guide
13 1 AFLP Preselective Amplification Preselective PCR Selective Amplification Preselective Amplification EcoRI MseI Selective Amplification PCR EcoRI/MseI Applied Biosystems EcoRI MseI-MseI Selective Amplification GeneMapper Software Version 4.0 AFLP Getting Started Guide 3
14 1 AFLP Data Collection Applied Biosystems Applied Biosystems GeneMapper Software Version4.0 Quick Reference Guide (PN ) AFLP GeneMapper AFLP Applied Biosystems AFLP Applied Biosystems Web ( 4 GeneMapper Software Version 4.0 AFLP Getting Started Guide
15 1 AFLP AFLP GeneMapper <drive>:\appliedbiosystems\genemapper\example Data\AFLP Data GeneMapper AFLP 5 FAM Applied Biosystems AFLP Plat Mapping Kit Applied Biosystems GeneScan -500 (ROX ) Applied Biosystems 3100 Panel Bin Set AFLP Panel Bin Set GeneMapper 14 Automatic Panel Generation GeneMapper Software Version 4.0 AFLP Getting Started Guide 5
16 1 AFLP AFLP 1-5 AFLP 2 AFLP 1. Panel Samples 4. Table Settings BinSet Bin AFLP 6 GeneMapper Software Version 4.0 AFLP Getting Started Guide
17 1 GeneMapper GeneMapper 1-1 Bin/ Bin Set/ Kit/ Marker / Panel/ RFU Analysis Method GeneMapper Bin Marker Bin ) Panel 2 DNA Marker Marker bp AFLP bp Marker Relative Fluorescent Units GeneMapper 1. GeneMapper v4.0 Start Programs Applied Biosystems GeneMapper GeneMapper v Login to GeneMapper User Name Password 3. OK AFLP GeneMapper Sofware Online Help GeneMapper v3.7 GeneMapper v3.7 GeneMapper v3.7 GeneMapper v3.7 AFLP GeneMapper Software Version 4.0 AFLP Getting Started Guide 7
18 1 GeneMapper AFLP GeneMapper AFLP 2 GeneMapper Data Collection AFLP GeneMapper Software Version 4.0 Installation and Administration Guide (PN ) GeneMapper 2 AFLP GeneMapper GeneMapper Software Version 4.0 Installation and Administration Guide (PN ) 8 GeneMapper Software Version 4.0 AFLP Getting Started Guide
19 Analysis Method GeneMapper Software Version 4.0 AFLP Getting Started Guide 9
20 2 Analysis Method AFLP GeneMapper Sofware Online Help vii GeneMapper AFLP Analysis Method Panel Bin Set GeneMapper GeneMapper Software Installation and Administration Guide (PN ) 1. GeneMapper 7 2. GeneMapper File New Project 3. New Project AFLP OK GeneMapper v3.7 4 AFLP GeneMapper Software Version 4.0 AFLP Getting Started Guide
21 2 GeneMapper AFLP (*.fsa) GeneMapper Samples GeneMapper GeneMapper Software Installation and Administration Guide (PN ) 1. File Add Samples to Project 2. Add Samples to Project Files 3. Example Data <drive>:\appliedbiosystems\genemapper\example Data\ 4. AFLP 5. Add to List >> AFLP Tutorial 6. Add Analysis Method GeneMapper Software Version 4.0 AFLP Getting Started Guide 11
22 2 Analysis Method Analysis Method Analysis Method Analysis Method Panel Bin Set Analysis Method Analysis Method GeneMapper Peak Quality Process Quality Analysis Method Panel Bin AFLP Analysis Method Analysis Method 1. GeneMapper Tools GeneMapper Manager 2. GeneMapper Manager Analysis Methods 3. Analysis MethodsNew 4. New Analysis Method AFLP OK 5. Analysis Method Editor General Analysis Method AFLP Tutorial Analysis Method Analysis Method Analysis MethodNew Analysis Method Analysis Method Analysis Method Allele Allele GeneMapper Automatic Panel Generation AFLP Allele 1. Analysis Method Editor Allele 2. Analyze Dyes Blue Analyze Dyes Blue FAM 12 GeneMapper Software Version 4.0 AFLP Getting Started Guide
23 2 Analysis Method 3. Analysis Range bp Analysis Range 50 bp 500 bp Analysis Range 4. Panel Generate panel using samples Panel 14 Automatic Panel Generation 5. Allele Calling AFLP a. Edit Labels b. Thresholds and Labels Details Thresholds c. Labels 0 2 Check 3 1 d. OK Name alleles using bin names Bin : bp Thresholds and Labels Details h h<50rfu 50 RFU h < 100 RFU h 100RFU 6. Allele Calling Delete common alleles 15 Delete Common Alleles Delete common alleles Peak Height Ratio Do not delete if Peak Height Ratio exceeds GeneMapper Software Version 4.0 AFLP Getting Started Guide 13
24 2 Analysis Method 7. Normalization a. Normalization Scope Project b. Normalization Method Sum of Signal 16 Normalization 7a 7b Normalization Method Genotypes Peak Detector Bin Set Analyze Dyes Panel Panel Normalization Allele Calling 2-6 AFLP Analysis Method Allele Calling Automatic Panel Generation Automatic Panel Generation AFLP Panel Bin AFLP AFLP Panel Bin Set Automatic Panel Generation Allele Panel Bin Set AFLP Panel Bin Set Panel Bin Set Panel Generation AFLP Panel Panel Panel A Panel P : P1-Dermis Panel 14 GeneMapper Software Version 4.0 AFLP Getting Started Guide
25 2 Analysis Method Samples user defined (UD) Panel B Panel Samples UD1 P1 P2 Panel Panel A B User defined (UD) 2-7 Panel A P B UD P1 P2 Delete Common Alleles Allele Calling Delete common alleles AFLP AFLP Bin Set 100 Delete common alleles Bin Delete common alleles Scope Within run Project Peak Height Ratio Peak Height Ratio Peak Height Ratio / Bin Allele Calling Analysis Method Analysis Method 1.8 Delete Common Alleles Peak Height Ratio 2-8 Allele Calling Peak Height Ratio GeneMapper Software Version 4.0 AFLP Getting Started Guide 15
26 2 Analysis Method AFLP Analysis Method AFLP AFLP GeneMapper 1. Normalization Method Sum of Signal Maximum Signal Normalization Scope Within Run Within Project 2. Normalization Scope 3. a. b. GeneMapper v4.0 Normalization Scope Normalization Scope None Within Run Project Normalization Method Normalization Method Normalization Scope Sum of Signal Normalization Scope 16 GeneMapper Software Version 4.0 AFLP Getting Started Guide
27 2 Analysis Method Maximum Signal Normalization Scope Normalization Scope Normalization Method 2-9 Peak Detector Peak Detector GeneMapper 1. Peak Detector 2. Peak DetectorPeak Detection Algorithm Advanced 3. Peak Detection Algorithm Advanced Peak Detection GeneMapper Software Online Help Peak Quality GeneMapper Software Version 4.0 AFLP Getting Started Guide 17
28 2 Analysis Method AFLP Peak Detection GeneMapper Range Peak Amplitude AFLP Ranges Ranges Raw Data 2 2 Analysis Range Raw Data Partial Range Start Pt Stop Pt Sizing Range Partial Range Start Size Stop Size Analysis Range Peak Detector Sizing Range 1 Peak Amplitude Thresholds Peak Amplitude Threshold Raw Data AFLP Peak Amplitude Threshold AFLP AFLP AFLP Peak Amplitude Threshold Peak Quality Peak Quality Genotypes PQV 1. Peak Quality 2. Peak Quality Quality Flags Peak Morphology Max Peak Width Broad Peak PQV (Check) Genotypes BD PQV 18 GeneMapper Software Version 4.0 AFLP Getting Started Guide
29 2 Analysis Method Pull-Up Ratio Pull-Up Ratio Genotypes SPU PQV (Check) Pull-Up Scan 3760 Pull-Up Scan Quality Flags Quality SettingsPQV 1. Quality Flags 2. Quality Flags Quality 3. OK AFLP Tutorial Analysis Method 4. Done GeneMapper Manager Quality Flag Settings Quality Flag Settings PQV Genotype Quality (GQ) 0 1 PQV GQ = MQ (1 SPU) (1 BD) (1 OS) ) BD Broad Peak PQV Quality Flag Setting GQ Genotype Quality PQV MQ Marker Quality OS Off-Scale PQV Quality Flag Setting SPU Spectral Pull-Up PQV Quality Flag Setting BD GQ MQ OS SPU PQV GeneMapper Software Version 4.0 Reference and Troubleshooting Guide (PN ) GeneMapper Software Version 4.0 AFLP Getting Started Guide 19
30 2 Analysis Method Max Peak Width BD (Broad Peak) GQ BD Quality Flag BD PQV BD Quality Flag Setting GQ PQV GQ GQ 0 PQV Thresholds PQV Thresholds SQ (Sizing Quality)GQ (Genotype Quality) (Pass) (Check) (Low Quality) SQ GQ 0 1 Analysis Method Peak Quality PQV Threshold PQV Threshold SQ GQ SQ/GQ v SQ GQ 0.75 v (Pass) 0.25 < v < 0.75 (Check) v 0.5 (Low Quality) 20 GeneMapper Software Version 4.0 AFLP Getting Started Guide
31 2 AFLP Tutorial Analysis Method GeneMapper GeneMapper Software Installation and Administration Guide (PN ) Table Setting AFLP Default Table Setting Samples Genotypes AFLP Table Settings vi GeneMapper Software Online Help AFLP Default Table Setting Table Setting AFLP Default AFLP Table Setting AFLP Default Table Setting 1. GeneMapperSamples a. Analysis Method AFLP Tutorial 12 b. Size Standard GS500(-250) AFLP Tutorial Analysis Method Panel Panel None 2. [Ctrl] Analysis Method Panel Size Standard GeneMapper Software Version 4.0 AFLP Getting Started Guide 21
![2 3. Edit Fill Down[Ctrl] + [D] Analysis Method Panel Size Standard 4.](/docs-images/104/162933306/images/32-0.jpg "3 Analysis Method Panel Size Standard / Analysis Method Analysis Range Sizing Range Analysis Method/Size Standard")
32 2 3. Edit Fill Down[Ctrl] + [D] Analysis Method Panel Size Standard 4. 3 Analysis Method Panel Size Standard / Analysis Method Analysis Range Sizing Range Analysis Method/Size Standard Analysis Method Analysis Ranges Sizing Ranges Panel Bin Set Analysis Method Bin Set Samples Panel Panel Panel/Bin Set 2-10 PQV 2-10 Alert 1. GeneMapper Samples 2. GeneMapper 3. Info 4. InfoError Message 5. Info Samples/Genotypes 22 GeneMapper Software Version 4.0 AFLP Getting Started Guide
33 Size Quality Panel Bin Set GeneMapper Software Version 4.0 AFLP Getting Started Guide 23
34 3 Samples Plot Genotypes Plot Bin Panel Manager Bin Samples Genotypes PQV Raw Data Plot Size Match Editor Samples Plot Genotypes Panel Bin Set AFLP AFLP GeneMapper Software Online Help vii 24 GeneMapper Software Version 4.0 AFLP Getting Started Guide
35 3 Automatic Panel Generation Samples Genotypes PQV Analysis Method Panel 13 4 Panel Bin Set Analysis Method Alleles 1 Marker Panel 0.8-bp Bin Panel Bin Set AFLP Bin Panel Manager AutoBin AutoBin AFLP Bin Analysis Method 13 6 Bin 1. Analyze Analyze 2. AFLP Tutorial OK 3. Analysis Completed Status Genotypes 4. Analysis Low Quality to Top Samples PQV GeneMapper Software Version 4.0 AFLP Getting Started Guide 25
36 3 5. Samples OS (Check) OS Process Quality Value (PQV) SQ (Check) 1 Genotypes Off-Scale PQV Check Sizing Quality PQV 6. Genotypes Panel Marker Panel Marker _Internal_Panel_ _Internal_Marker_Dye_Blue_ Panel Marker Panel Marker OSSQ (Pass) GeneMapper Software Version 4.0 AFLP Getting Started Guide
37 3 Samples Off-Scale (OS) PQV (Check) Raw Data Raw Data Raw Data Plot Info EPT Data1 PQV (Pass) OS PQV OS PQV OS PQV GeneMapper PQV Samples OS PQV Genotypes OS PQV OS (Check) Raw Data 1. GeneMapper Samples 2. GeneMapper AFLP OS (Check) 3. Raw Data Raw Data Project Raw Data 4. Raw Data Plot X ( ) GeneMapper Software Version 4.0 AFLP Getting Started Guide 27
38 3 5. Raw Data Plot FAM AFLP 1140 GeneScan -50 (ROX ) 1265 Selective Amplification 35-bp 34 #3: 35-bp RFU 8200 RFU AFLP Samples Samples Genotypes Size Quality 28 GeneMapper Software Version 4.0 AFLP Getting Started Guide
39 3 Size Quality Size Quality 3 #1: Analysis Method 30 #2: 32 #3: 34 GeneMapper Software Version 4.0 Reference and Troubleshooting Guide (PN ) SQ PQV GeneMapperSamples SQ PQV Sizing Quality Sizing Quality Sizing Quality 1 0 Quality Flags PQV Threshold 20 Sizing Quality (Pass) (Check) (Low Quality) Classic Sizing Quality SQ (Check) GeneMapper Sizing Quality 1. GeneMapper Edit Select All [Ctrl] [Select] 2. Analysis Size Match Editor 3. Size Match Editor 4. Size Matches X ( ) GeneMapper Software Version 4.0 AFLP Getting Started Guide 29
40 3 Size Quality 5. Y 1000 RFU a. View Y-Axis Scale Scale to b. Enter Maximum Y-Axis Value 1000 OK X Y bp 35-bp Sizing Quality 0.45 Sizing Quality Off-scale 35-bp Analysis Method #1: Analysis Method Analysis Method Analysis Method Analysis Range Start Point 6 1. Size Match Editor AFLP_sample_A01_001_ fsa bp bp OK Size Match Editor 4. AFLP Tutorial Analysis Method Samples Analysis 5. Analysis Method Editor Peak Detector 30 GeneMapper Software Version 4.0 AFLP Getting Started Guide
41 3 Size Quality 6. Peak Detector Ranges a. Analysis Partial Range b. Start Pt.1325 Analysis Range (Partial Range) Analysis Range Start Pt 35-bp 7. OK Analysis Method Analysis Method Status 8. Analyze Analyze 9. Analysis Low Quality to Top 10. Samples SQ (Pass) bp (Pass) Status bar (Analysis Complete) Genotypes PQV Pass GeneMapper Software Version 4.0 AFLP Getting Started Guide 31
42 3 Size Quality #2: AFLP_sample_H02_016_ fsa 35-bp 1. GeneMapper Edit Select All 2. Analysis Size Match Editor 3. Size Match Editor AFLP_sample_H01_015_ fsa 35-bp 3-11 AFLP_sample_H01_015_ fsa AFLP Samples SQ (Pass) Size Match Editor 35-bp Analysis Range Start Point Sizing Quality 35-bp 3-11 AFLP_sample_H01_015_ fsa 35-bp Sizing Quality Sizing Quality Analysis Method Sizing Quality PQV Pass Range SQ (Pass) 20 PQV Thresholds 32 GeneMapper Software Version 4.0 AFLP Getting Started Guide
43 3 Size Quality 1. Size Match Editor AFLP_sample_H01_015_ fsa bp a. 35-bp b. Delete Edit Delete Size Label bp a. 35-bp b. Edit Add Size LabelAdd c. Select Size bp 4. Tools Check Sizing Quality Sizing Quality Sizing Quality 35-bp 5. ApplyOK Apply GeneMapper Software Version 4.0 AFLP Getting Started Guide 33
44 3 Size Quality 6. Samples AFLP_sample_H02_016_ fsa Status (Reanalyze) SQI SQ (Pass) SQI PQV SQ PQV 7. Analyze Analyze #3: 35-bp 30 #1: Analysis Method #1 #3 35-bp GeneMapper 2 : bp Applied Biosystems GeneMapper 1 34 GeneMapper Software Version 4.0 AFLP Getting Started Guide
45 3 Size Quality GS500(-250) 35-bp 35-bp 35-bp 250-bp bp bp / 1. GeneMapper Tools GeneMapper Manager 2. GeneMapper Manager Size Standards 3. New Samples Size Standard New Size Standard Size Standard 4. Select Dye and Analysis Method Basic or Advanced OK 5. Size Standard Editor a. NameAFLP50-500(-250) b. Size Standard Dye Red c. Size Standard [Enter] 500 [Enter] GeneMapper Software Version 4.0 AFLP Getting Started Guide 35
46 3 Size Quality Analysis Method Allele Peak Detector Analysis Range Sizing Range OK 7. Done GeneMapper Manager 1. Analysis Method a. SamplesAnalysis AFLP Tutorial Analysis Method b. Analysis Method Editor Peak Detector c. Ranges Analysis Full Range d. OK Analysis Method Analysis Method Editor Analysis Range (Full Range) 2. GeneMapper Samples 3. Size StandardAFLP50-500(-250) GeneMapper Software Version 4.0 AFLP Getting Started Guide
![3 Size Quality 4. a. Size Standard b. Edit Fill Down [Ctrl]+[D] 5. Analyze Analyze 6.](/docs-images/104/162933306/images/47-0.jpg "Samples PQV SFNF MNF SNF OS SQ (Pass) GeneMapper 7. Size Match Editor 8. 38 GeneMapper Software Version 4.")
47 3 Size Quality 4. a. Size Standard b. Edit Fill Down [Ctrl]+[D] 5. Analyze Analyze 6. Samples PQV SFNF MNF SNF OS SQ (Pass) GeneMapper 7. Size Match Editor GeneMapper Software Version 4.0 AFLP Getting Started Guide 37
48 3 GeneMapper 1. Genotypes PQV Samples Plot Samples Plot 42 GeneMapper Bin Panel Bin Set Size Match Editor GeneMapper Genotypes Genotypes Genotypes Genotypes PQV Genotypes PQV 1. GeneMapper Genotypes Panel Marker Panel _Internal_Panel_ Marker _Internal_Marker_Dye_Blue_ 2. Genotypes Bin Set Bin 1 Allele Size Height Bin Analysis Method Label 12 Allele : bp : RFU Peak Area Data Point 38 GeneMapper Software Version 4.0 AFLP Getting Started Guide
49 3 3. Analysis Low Quality to Top 4. Genotypes Genotypes PQV AE OS SPU AN BD GC Samples PQV (Pass) (Check) (Low Quality) PQV OS (Pass) (Pass) Analysis Method Analysis Range GQ (Pass) PQV Analysis Method Pass Range Genotype PQV 20 PQV Thresholds PQV Samples Plot Samples Genotypes GeneMapper Software Online Help vii Genotype PQV GeneMapper Software Version 4.0 Reference and Troubleshooting Guide (PN ) Samples Plot Samples Plot Samples Plot GeneMapper Panel Bin Set GeneMapper Software Version 4.0 AFLP Getting Started Guide 39
50 3 Samples Plot Genotypes Plot Genotypes Samples Plot Genotypes Plot AFLP Plot Genotypes Plot Samples Plot AFLP Samples Plot Genotypes Plot GeneMapper Sofware Online Help vii Plot Settings Plot Settings Samples Plot Genotypes Plot AFLP Plot Settings AFLP DefaultAFLP Default Plot Settings Plot Settings Help Contents and Index GeneMapper Sofware Online Help Samples Plot Samples Plot Samples Genotypes SamplesGeneMapper 1. GeneMapper Samples 2. SamplesEdit Select All 3. Analysis Display Plots 4. AFLP Samples Plot a. Plot Setting AFLP DefaultAFLP b. Panes 22 c. View Tables Genotypes Table Samples Plot Genotypes bp a. X Zoom to b. X-Axis Zooming minimum maximum OK c bp RFU a. Y Zoom to b. Y-Axis Zooming Zoom To 500 Apply to all electropherograms OK 40 GeneMapper Software Version 4.0 AFLP Getting Started Guide
51 3 7. Bin Delete common alleles Bin 13 6 : bp : RFU Marker / Alleles Analysis Method Marker Marker Peak Selection Samples Plot Peak Selection Binning Samples Plot Bin Marker Peak Selection Bin Sample Plot X bp Y RFU Marker Bin ) Genotypes GeneMapper Software Version 4.0 AFLP Getting Started Guide 41
52 3 Samples Plot Bin 3 0 Check Bin Bin Analysis Method Analysis Range 3-13 A Delete common alleles 13 6 Bin Marker Marker Analysis Method Analysis Range Marker bp Marker 50 bp 500 bp Analysis Method Analysis Range Analysis Method B(lue) Peak Amplitude Threshold A A A 3-13 Samples Plot 2 1. Samples Plot Panes 1 2. Samples Plot a. (Red signal) View Dyes Red Dye b. (Blue signal) View Dyes Blue Dye 3. View Tables Sizing Table Samples Plot Sizing 42 GeneMapper Software Version 4.0 AFLP Getting Started Guide
53 3 4. View Plots Overlay All bp a. X Zoom to b. X-Axis Zooming minimum maximum OK RFU a. Y Zoom to b. Y-Axis Zooming Zoom To 500 OK 7. Samples Plot 1 Sample Plot 8. File Close Plot Window [Esc] 44 GeneMapper Software Version 4.0 AFLP Getting Started Guide 43
54 3 AFLP 1. SamplesEdit Select All 2. Analysis Display Plots 3. AFLP Samples Plot a. View Tables Genotypes Table Genotypes b. View Plots Overlay All c. View Bins Bin bp a. X Zoom to b. X-Axis Zooming minimum maximum OK RFU a. Y Zoom to b. Y-Axis Zooming Zoom To 800 OK 6. a. View Plot Colors Custom b. View Legends GeneMapper Software Version 4.0 AFLP Getting Started Guide
55 Bin Set Panel 1 Tools Plot Settings ) Plot Settings Editor Display Settings (Custom Colors) Genotypes GeneMapper Software Version 4.0 AFLP Getting Started Guide 45
56 3 Samples Plot Panel Bin Set Marker 46 Bin Samples Plot Bin Marker 51 Panel Bin Set Samples Plot Genotypes Plot Genotypes Plot Marker Marker Marker Samples Plot Binning ( ) 1. View Plots Separate Dyes 2. Panes Samples Plot Alleles Editing Mode Binning Binning 4. _Internal_Marker_Dye_Blue_ Marker 5. Marker 6. Marker 7. Marker Marker 8. Panel a. File Save Panel b. Save Panel Save Panel OK c. Save Panel OK 9. View Plots Overlay All 46 GeneMapper Software Version 4.0 AFLP Getting Started Guide
57 3 Bin Bin Set Bin Bin Samples Plot Binning 1. Samples Plot Bin 2. View Plots Separate Dyes 3. Panes Samples Plot Alleles Editing Mode Binning Binning 5. Sample Plot Bin 6. _Internal_Marker_Dye_Blue_ Marker 7. Bin a. Add Bin b. c. Add Bin Bin : bp : bp Marker Bin d. OKBin Bin Bin Edit Bin GeneMapper Software Version 4.0 AFLP Getting Started Guide 47
58 3 8. Bin a. Bin b. Bin Binning Marker Blue Bin 37 Bin Right offset Bin Bin Delete BinBin 9. Panel a. File Save Panel b. Save Panel Save Panel OK c. Save Panel OK 10. View Plots Overlay All 1. a. View Bins Bin b. Samples Plot c. 2. View Plots Separate Dyes 3. Panes 2 4. Samples Plot Alleles Editing Mode Peak Selection Peak Selection Sample Plot 1 48 GeneMapper Software Version 4.0 AFLP Getting Started Guide
59 Add Allele Call 3. Add Allele Comment OK Peak Selection Bin bp bp View Plots Overlay All PQV Modified Check Rename Allele Custom 3. Create Custom Allele Name OK GeneMapper Software Version 4.0 AFLP Getting Started Guide 49
60 3 4. Edit Allele Comment OK Bin bp bp 5. View Plots Overlay All View Plots Separate Dyes 3. History 4. Allele History OK 5. View Plots Overlay All 50 GeneMapper Software Version 4.0 AFLP Getting Started Guide
![3 Panel Bin Set Panel Bin Set GeneMapper Panel Bin Set AFLP Tutorial Panel Bin Set GeneMapper Panel Bin Set Panel Bin Set Panel 1. File Close Plot Window [Esc] Samples Plot 2.](/docs-images/104/162933306/images/61-0.jpg "GeneMapper File Export Project Panel 3. Specify Names a. Chemistry Kit NameAFLP Tutorial Kit b. Panel NameAFLP Tutorial Panel c. OK 4.")
61 3 Panel Bin Set Panel Bin Set GeneMapper Panel Bin Set AFLP Tutorial Panel Bin Set GeneMapper Panel Bin Set Panel Bin Set Panel 1. File Close Plot Window [Esc] Samples Plot 2. GeneMapper File Export Project Panel 3. Specify Names a. Chemistry Kit NameAFLP Tutorial Kit b. Panel NameAFLP Tutorial Panel c. OK 4. Select Export Folder ExportPanel Panel Panels <drive>:\appliedbiosystems\genemapper\panels 5. GeneMapper Tools Panel Manager 6. Panel AFLP Tutorial Kit_Panel.txt a. Panel Manager Panel Manager b. File Import Panels c. Import Panels AFLP Tutorial Kit_Panel.txt Import AFLP Tutorial Kit AFLP Tutorial Panel _Internal_Marker_Dye_Blue_ marker Kit Panel Marker GeneMapper Software Version 4.0 AFLP Getting Started Guide 51
62 3 Panel Bin Set 7. Bin Set AFLP Tutorial Kit_Bin.txt a. AFLP Tutorial Kit b. File Import Bin Set c. Import Panels AFLP Tutorial Kit_Bin.txt Import 8. Apply AFLP Tutorial Panel Bin Set Panel Makrer GeneMapper Bin Set 1. Panel Manager a. AFLP Tutorial Kit Kit b. AFLP Tutorial Panel Panel Bin Set Bin Set Panel Manager Panel Bin Set Panel 2. Panel Bin a. AFLP Tutorial Panel Blue Marker Panel Blue Marker Bin Set b. X Scale to c. X-Axis Scale Minimum Maximum OK Bin Marker Marker Bin (52) 3. Marker Bin Bin Marker / Marker Marker Marker Analysis Method Analysis Range 17 Peak Detector 52 GeneMapper Software Version 4.0 AFLP Getting Started Guide
63 3 Panel Bin Set Bin Set Bin Samples Plot Panel Manager bp Bin a. Panel Manager Plot New Bin b. 54 bp c. Add Bin to "Blue" NameCustom Location54 Bin Marker Bin Bin bp d. OKBin 2. Custom Bin 1 bp a. Bin Bin Edit Bin ) b. Edit Bin Left offsetright offset 0.5 OK Bin Bin Bin Custom Bin Bin } Right offset Bin 3. Custom Bin Delete Bin Bin 4. Panel Manager OK Analysis Method Panel Panel Analysis Method Bin Set AFLP Tutorial Analysis Method Bin Set Analysis Method Bin Set 1. GeneMapper Tools GeneMapper Manager 2. GeneMapper Manager Analysis Methods 3. AFLP Tutorial Open GeneMapper Software Version 4.0 AFLP Getting Started Guide 53
![AFLP Tutorial Panel Panel 3. a. Panel b. Edit Fill Down [Ctrl] +[D] 4.](/docs-images/104/162933306/images/64-2.jpg "Analyze Analyze AFLP Tutorial Panel 54 GeneMapper Software Version 4.")
64 3 Panel Bin Set 4. Allele a. Panel Use specified panel Bin Set Bin Set b. Bin Set AFLP Tutorial Kit_Bin_Set Bin Set Bin Set Use specified panel 5. OK AFLP Tutorial Analysis Method 6. Done GeneMapper Manager Panel 1. GeneMapper Samples 2. Panel a. Panel b. Select a Panel AFLP Tutorial Kit c. AFLP Tutorial Panel Panel 3. a. Panel b. Edit Fill Down [Ctrl] +[D] 4. Analyze Analyze AFLP Tutorial Panel 54 GeneMapper Software Version 4.0 AFLP Getting Started Guide
65 3 4 GeneMapper GeneMapper Analysis Method Allele Analysis Method GeneMapper Software Version 4.0 AFLP Getting Started Guide 55
66 3 56 GeneMapper Software Version 4.0 AFLP Getting Started Guide
67 Samples Genotypes GeneMapper Software Version 4.0 AFLP Getting Started Guide 57
68 4 Samples Genotypes Report Manager GeneMapper AFLP GeneMapper Sofware Online Help vii 58 GeneMapper Software Version 4.0 AFLP Getting Started Guide
69 4 GeneMapper GeneMapper 4-2 GeneMapper / GeneMapper Samples Genotypes 60 Samples Report Manager 61 Genotypes Samples Plot 60 Sizing 60 Genotypes Genotypes Plot 60 GeneMapper Manager Analysis Methods Table Settings Plot Settings Report Settings GeneMapper Manager 60 Genotypes GeneMapper Report Manager AFLP AFLP Genotypes Microsoft Excel Genotypes 61 GeneMapper Software Version 4.0 AFLP Getting Started Guide 59
70 4 Samples Genotypes Samples Genotypes Samples Genotypes Export Table 61 Samples Genotypes 1. GeneMapper Samples Genotypes 2. File Export Table File Export Combined Table Export Combined Table Samples Alt-Print Screen GeneMapper Windows OS Ctrl-Print Screen Alt-Print Screen [Alt] [Print Screen] Windows OS 3. Microsoft Word Excel 60 GeneMapper Software Version 4.0 AFLP Getting Started Guide
71 4 Report Manager Samples Genotypes Report Manager Samples Genotypes Report Manager Calculation Analysis Custom Report Setting 1. a. GeneMapper Genotype Allele b. 2. Tools GeneMapper Manager 3. GeneMapper Manager Report Settings New Report Settings Editor 4. NameAFLP Tutorial 5. Number of Alleles 1 6. Genotypes Report Setting a. Available Columns Genotype b. [Ctrl] [Shift] Sample File Sample Name Sample IDAllele 1 Allele 59 c. d. OK Report Setting 7. Done GeneMapper Manager 1. GeneMapper Edit Select All 2. Analysis Report Manager 3. Report Manager Report Setting AFLP Tutorial Report Setting AFLP GeneMapper Software Version 4.0 AFLP Getting Started Guide 61
72 4 4. Edit Flip Table 5. a. Report Manager File Export Table b. Export Report Desktop c. File nameaflp Tutorial d. Export File As Tab-delimited text (.txt) Comma-separated values (.csv) e. Export 6. Report Manager a. File Save b. Save AFLP Tutorial OK 7. Report Manager File Exit 62 GeneMapper Software Version 4.0 AFLP Getting Started Guide
73 4 GeneMapper Manager Panel Manager GeneMapper GeneMapper GeneMapper Manager Panel Manager AFLP Kit Panel Bin Set 1. GeneMapper Tools Panel Manager Panel Manager 2. Panel Manager Kit Panel Bin Set File Export Panels Bin SetAll Kits Analysis Method 1. GeneMapper Tools GeneMapper Manager GeneMapper Manager 2. GeneMapper Manager Export GeneMapper Analysis Method Panel 1. GeneMapper Tools GeneMapper Manager GeneMapper Manager 2. GeneMapper Manager Projects Export GeneMapper Software Version 4.0 AFLP Getting Started Guide 63
74 4 4-3 GeneMapper 4-3 GeneMapper Samples Genotypes Sample File Info Raw Data EPT Data Samples Plot 1. GeneMapper 2. File Print 3. GeneMapper File Print 6. GeneMapperSamples 7. Samples Samples Plot 8. Analysis Display Plots 9. Genotypes Plot 10. File Print 11. GeneMapperGenotypes 12. Genotypes Genotypes Plot 13. Analysis Display Plots File Print 64 GeneMapper Software Version 4.0 AFLP Getting Started Guide
75 _Internal_Marker_Dye_Blue_ 26 _Internal_Panel_ 26 A Allele Calling 13 Allele 38 Allele 12 amplified fragment length polymorphism (AFLP) 2 Analysis Method 12 Allele 12 Peak Detector 17 Peak Quality 18 Quality Flags 19 Panel Analysis Range 13, 18 Analyze Dyes 12 Applied Biosystems vii vii vii Automatic Panel Generation 14, 25 B Bin 7, 41, 42, 52 47, 53 Bin Set 7, 52 D Data Collection 4 Data Point 38 Delete common alleles 13, 15 G GeneScan-500 (ROX) 5 Genotype Quality (GQ) 19 Genotypes 38 GQ 39 H Height 38 K Kit 7 M Marker 7 Marker 46 Max Peak Width 18 MSDS vii N Name alleles using bin names 13 Normalization Method 14, 16 Normalization Scope 14, 16 O OS PQV 27 OS 26, 39 P Panel , 25 PanelMarker 26 Panel 51 Peak Amplitude Thresholds 18 Peak Area 38 Peak Detector 17 Peak Height Ratio 15 Peak Quality 18 Peak Selection 41 Plot Settings 40 PQV Thresholds 20 Preselective Amplification 3 Pull-Up Ratio 19 Q Quality Flag Settings 19 R Ranges GeneMapper Software Version 4.0 AFLP Getting Started Guide 65
76 Raw Data 27 S Sample Plot 39 Selective Amplification 3 Size Match Editor 29 Size 38 Sizing Quality 30 Sizing Range 18 SQI 34 SQ PQV 29 SQ 26, 31, 34 Status 34 T Table Setting 21 Thresholds and Labels Details / Panel vii 27 vii 6 44 vi AFLP 2 4 v Analysis Method Panel Generation v v! v v v v 66 GeneMapper Software Version 4.0 AFLP Getting Started Guide
77 v Panel Bin Set 51 Raw Data v v v v v vii ii GeneMapper Software Version 4.0 AFLP Getting Started Guide 67
78 68 GeneMapper Software Version 4.0 AFLP Getting Started Guide
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isplever CLASIC 1.2 Startup Manual for MACH4000 Rev.1.0 isplever_ CLASIC Startup_for_MACH4000_Rev01.ppt Page: 1 1. Page 3 2. Lattice isplever Design Flow Page 4 3. Page 5 3-1 Page 6 3-2 Page 7 3-3 Page
Infoprint 250 GA
Infoprint 250 GA88-0164-00 Infoprint 250 GA88-0164-00 ! viii 2000 5 Copyright International Business Machines Corporation 2000. All rights reserved. ii Infoprint 250 ...III... VI...VII... VIII... VIII...IX
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(1) (2) Play Volume (3) (4) (5) (6) (7) (8) Ctrl N Ctrl Ctrl (9) (10) OFF (11) (12) OFF (13) (14) 2 3 4 5 6 7 LCD LCD 8 TV ANT. S IN VIDEO IN LINE-L IN LINE-R IN 9 10 11 12 LCD LCD 13 LCD 14 LCD 15 LCD
これわかWord2010_第1部_100710.indd
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パワポカバー入稿用.indd
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