GeneMarker HID Quick Start

Transcription

1 GeneMarker HID Quick Start Guide

2 Upload Data Run Wizard Size Call Quality Review Edit Panel Compare & Analyze Save & Print Reports SoftGenetics Relationship Testing

3 Start Your Project Open Data Open Data Files Add Select files to add (Ctrl+A) Open (Files are added to list) OK Chapter 2

4 Synthetic Gel Image Sample File Tree Electropherogram

5 Run Run Run Wizard Template Selection Panel select from drop-down menu Size Standard select from drop-down menu Standard Color select from drop-down menu Next Chapter 2

6 Run Wizard Data Process Load Default Run Wizard Data Process Next Chapter 2

7 Run Wizard Additional Settings OK Ensure Auto Select Best Ladder and Auto Panel Adjustment are selected Run Wizard Additional Settings Data Processing OK (when analysis has finished) Chapter 2

8 Run Wizard Icon Main Toolbar Icons Report Table Size Called Samples Green = High Lane Quality Yellow = Requires Verification Red = Sizing Did Not Occur Electropherograms Project Summary

9 Zoom in In electropherogram, hold left-click and drag a box from upper left to lower right Zoom out In electropherogram, hold left-click and drag a box from lower right to upper left Scroll In electropherogram, hold right-click and drag trace right or left Navigation One Color Viewing - Click the Show Color icon Hide Panels - Click the Show/Hide icons Chapter 3

10 Calibration Charts Select Size Calibration icon In Sample Trace Right Click Add or delete peaks (if necessary to improve score values) In Sample Trace Right Click Update Calibration Close Calibration Charts window Chapter 4

11 Panel Editor Tools Menu Panel Editor Select PanelName From Panel Templates Verify markers and bins align with peaks virtual (variant) alleles should have Control column designation = 0, major alleles of the ladder control column designation = 1 Double-click Locus (Marker) - Set Intensities, Imbalance, and Stutter Filters for each locus or Apply to All Markers Click OK Save with Signal Information to calibrate the panel Right mouse click on panel name and select Set as Project Panel Automatically applies any panel edits to the project Chapter 5

12 Browse by All Color Icon Applications Profile Comparison View Chapter 3

13 Actions Automatically Recorded Updates Allele Report

14 Save Report Table Click Report Settings icon Select Peak Table Click OK Save as Text File Click Save Report icon Specify the directory and report title Reporting To open report in Excel: Open report Delimited, Tab, General Finish Chapter 6

15 Export to CODIS Applications Export CODIS Edit header information Click cell in table to activate dropdown menu options Click OK Export to CODIS Save As Select directory and enter file name Click Save (saves as CMF 3.2.xml and CMF 1.0.dat files) Chapter 6

16 Allele Report Project Print Report Preview Content Options (choose print settings) Print Print and Save Save Project File Save Project Chapter 6

17 Main Screen Detect mixtures and peak ratios Chapter 7

18 Applications Mixture Analysis Automated mixture analysis Determins number of contributors All possible allele combinations Identifies major and minor contributors Easy to set analysis parameters Likelihood Ratios calculated Toggle to display LR or Traces Save to and Search database Chapter 7

19 Main Analysis Window Select Relationship Testing from Applications Select Parameters for analysis Okay Automatic Pedigree Drawing Tools Family Group Tool Match and then OK Chapter 8

20 Tool Bar Icons Conflict with parents Conflict with siblings Linked Information Conflict identified in list genotype Conflict linked to electropherogram Chapter 8

21 Tool Bar DataBase dropdown menu Edit or Save to Database Tools select allele frequency Right click on node Activates dropdown Select Find Family from node on pedigree or on single sample Report kinship calculations from all database samples Displays: Same sample match(es) Highest combined LR for each relationship level Chapter 8

22 Tool Bar Tools Kinship Analysis Select parameters Sample file choices Current project files automatically available Load from.txt file Load from database Dropdown menu Select file for individual A Select file for individual B Right click on table to Copy/Paste into existing report, or Save Kinship analysis Need Help? 30-day Free technical assistance Tech_support@softgenetics.com Chapter 8