User Guide for the Genetic Analysis Lab Information Management System (dnalims)

Transcription

1 UNIVERSITY CORE DNA SERVICES University Core Genetic Analysis Laboratory Faculty of Medicine Health Sciences Centre, Rm. B104A Tel: (403) , Fax: (403) , or User Guide for the Genetic Analysis Lab Information Management System (dnalims) Retrieving and Viewing Sequencing Results File: Retrieving and Viewing Results dnalims User Guide.doc, Log on to 1. Using your Internet browser, go to 2. Log in with your Login Name & Password. If you have forgotten this information, use the Forgot Your Login Information? hyperlink to have this information automatically sent to you by The main dnalims User Tools menu will appear 3330 Hospital Drive N.W., Calgary, AB, Canada T2N 4N1

2 Downloading and Viewing DNA Sequencing Results 1. From the main dnalims User Tools menu, select the Download Your DNA Results hyperlink. This will display the Download DNA Sequencing Results page Results may be retrieved by either the Order number (assigned when you submitted your request) or by Plate number (assigned by Sequencing Lab staff). 3. Select your order or plate number from among the lists on the right-hand side or type in an order or plate number in the column on the left-hand side. 4. Click Submit. 2

3 3 5. A new Download Sequencing Results page will appear containing two tables. 6. The upper table called Sequencer Output is used to download all of the files in one operation. A compressed zip archive is created for the download. Choosing Text downloads all of the *.seq files containg the results in ASCII text. Choosing Chromat downloads chromatogram (or trace) files in *.ab1 binary format. Note for Windows XP users: To extract files from a zipped compressed folder 1. Open My Computer, and then locate the compressed folder. 2. Do one of the following: o o To extract a single file or folder, double-click the compressed folder to open it. Then, drag the file or folder from the compressed folder to a new location. To extract all files or folders, right-click the compressed folder, and then click Extract All. In the Compressed (zipped) Folders Extraction Wizard, specify where you want to store the extracted files. 7. The bottom table lists each sample individually. Use the Text, Chromat or View hyperlinks in the bottom table to download or view each sample individually. o Text displays the result as the ASCII text sequence in a.seq file. To save this result as a file, you must right-click on the link and select Save link target as o Chromat displays the result as the binary.ab1 file. To save this result as a file, you must right-click on the link and select Save link target as. o View displays the sequencing result using the viewer built into the dnalims. 3

4 8. Once the results have been transferred to your computer, the.seq and.ab1 files can be manipulated with a variety of software. The.seq text files can be used in any word processing or text editors, although you will need to assign the.seq file type to your text editor to be able to launch it just by double-clicking on the file. The.ab1 Chromat or trace files are the binary data files containing the electropherogram results read by the sequencer. Although, the dnalims contains a built-in trace view (see below), we recommend use of Sequence Scanner from Applied Biosystems (Windows only) or Finch TV from Geospiza (Mac and Windows). Both of these trace viewers are freeware and links to them can be found on our web site at Sequence Scanner is particular useful because it has the ability to create pdf files of the sequencing traces (without having to purchase Adobe Acrobat) and the ability to compare multiple files. 4 The dnalims Built-in Sequence Viewer (Click on View to launch the built in viewer) This built in trace viewer has many different functions and allows you to view and edit your sequence. With the Utilities buttons, you can: o View the unedited data (Edited Sequence box not checked). o Edit the sequence (Edited Sequence box checked) - double click on a single base to open a text box to make changes. o View summary the full sequence in one pane for overall view of signal strength. o View reverse complement. 4

5 5 With the Next N button you can find peaks which could not be based called by the original UCDNA Analysis software. You may then edit or manually call these bases. With Find - search for specific sequences. To change the viewing parameters use the Screen, H (horizontal peak spacing) and V (vertical peak height) options. Click the Sequence Text button to view your text in the box below, use this text box to copy contents to your computers clipboard for further data analysis. With Data: Select/highlight a base, then select the data button to display information related to that particular base. Data View will display the relative signal intensity of each of the nucleotides in the highlighted base position from eleven different points. It also displays left and right slopes and deviation. 5

6 6 Downloading and Viewing DNA Fragment Analysis Results 1. From the main dnalims User Tools menu, select the Download Fragment Analysis Results hyperlink. This will display the Download Fragment Analysis Results page. 2. Select or type in the order number of your request or, for 96 well plate requests, the plate number. 3. Click Submit. 6

7 7 4. On the Download Fragment Analysis Results page, use the top table (Chromat button) to download all the files together or use the bottom table to download individual files. 5. The Chromat file contains the trace data and can be viewed using the built in viewer or another program of your choice. The dnalims Built-in FSA FileViewer (Click on View FSA File to launch the built in viewer) This built in viewer has an automatic scan function, but still maintains some manual function if desired. Click on the scan window to activate it, choose automatic or manual scan, and then select the Begin Scan button. You will be prompted for a standard, and then the program will perform the analysis. The color buttons under the toolbar allow you to choose which colors you would like to view, and the zoom control is located on the right hand side of the window. Checking the Summary View box will condense the trace so it can be viewed without scrolling. The Rescan Peak button will allow you to redo the analysis. 7