1. How to Login Login to GeneSifter using your assigned user name and password:

Username: First name (underscore) Last name Password: randomly generated

2. How to Navigate the site

a. Return to the home page at any time by clicking the Home tab b. Click on any of the hyperlinks in the menu on the left c. Click on any of the hyperlinks in the Dashboard Boxes

3. How to edit your User Profile information

a. How to Change your assigned password

i. Click on the hyperlink of your name, located at the top right of home screen

ii. Click on the Edit user button

iii. Edit Password (no spaces, must contain a number) iv. Confirm Password v. Edit any other information

vi. Click Update User Button

a.

b.

c.

b. How to add a Billing Address. (You will be prompted to add a Billing Address when

entering your first order.) A Billing Address can be selected as a Default which will be pre-populated on a drop-down menu on future Orders.

i. Click Add billing address button

ii. Internal Users: put the address of the Facility, as well as our email address: dnanalysis@yale.edu. This information is required by the System but is not necessary for our Internal users.

iii. External Users: Paper copies of Invoices are no longer mailed. The MOST

critical piece of information is the email address. Invoices are sent at the end of each billing cycle to this email address(es) as pdf’s.

iv. Edit information and click Save Address

4. How to place an Order

a. Click on the Place Order link in the navigation menu

b. Select the service of choice by clicking on the picture icon or the Text

description. It is very important to select the correct service! Please read the description of services or call us if you have a question.

c. Fill in the Order information (all fields with * must contain text.)

d. Fill in the Sample Information by using the default web form or the excel sheet.

Pay Special attention to these Icons:

Fill Down: Copies/repeats Fill Down Plus: Fills in a chronological series

A chronological series can be filled by typing a number (and text) in the template field and clicking the Fill Down Plus icon below the template field

i. If individual wells need editing, double click in the field and edit. ii. When Finished Click Next

e. Using the Excel Feature to download/upload an excel spreadsheet rather than using the web page form.

i. Click the button to download the Finch excel template, GeneSifter_InputGrid.xls

ii. Edit the template and primer columns as needed. Leave blank wells

without text otherwise a charge will automatically be applied for those samples. Edit other columns on web form after upload to avoid error messages.

iii. Save the edited sheet on your computer, the name of the file does not have

to change.

iv. Click the button to upload the excel template. A window will appear.

v. Choose File and Click Upload. (if an error message appears then an

offending character may be in the file name (only text and numbers are allowed). If there are still errors appearing try another browser (Firefox or Internet Explorer sometimes work better then Safari.)

vi. Click Close

vii. Edit web form as needed and verify that sample names were uploaded correctly

viii. Click Next at the bottom of the page

5. How to edit Purchasing Information

The Submit Order button is only activated after purchasing information has been entered. Click on the purchasing information hyperlink.

Internal Users:

a. Select PTAEO Yale Charging Instructions from the drop down menu in the Charge Code

Type Field

b. In the field enter your PTAEO. The PTAEO format must be entered correctly or an error message will appear. A decimal point should separate each of the fields.

1234567.00.12345A.834500.123456

i. Project: always 7 numeric values (example: 1234567)

ii. Task: varies (example: 00, PROJ2) iii. Award: always 6 alphanumeric values (examples: N12345, 12345A) iv. Expenditure: always 834500 v. Organization: always 6 numeric values (example: 123456)

c. Click the Save & Next button d. Click the activated Submit Order button

External Users:

a. Select Purchase Order from the drop down menu in the Charge Code Type Field

b. In the field enter your purchase order number. c. Click Save & Next d. Click the activated Submit Order button

6. How to Quickly evaluate the Quality of a Chromatogram

a. Take a look at the Quality Scores. This is by no means an absolute on success or

failure, but a Q20/len score above .70 generally indicates a “passing” read. That Number is a determined by dividing the Len (overall length, but remember we don’t “trim” anything) by the Q20.

What is a Q20 anyway? It’s a universal code based on the Phred quality scores. Quality scores range from 4 to about 60, with higher values corresponding to higher quality. The quality scores are logarithmically linked to error probabilities, as shown in the following table:

a. Look at the Quality Graph, a better indication of quality

i. This is an example of a high quality long sequence with high quality

scores

ii. This is an example of a failed sequence (very low quality scores)

b. Take a look at the Chromatogram, the best indication of quality.

7. How to download .ab1 files

a. From the home page, select the underlined number to the right of Folders under the My Data Dashboard

b. Click on the number in the Chromats column associated with the order of interest

to view files.

c. At the Contents of folder page you can:

• Download Chromats (in several formats) • View a Folder report • View individual chromatograms

Download all data in a folder Click the Download Chromats button. Limitations can be set by selecting other options from the drop down menu.

Download one chromatogram

Click the Download Sequences button. Limitations can be set by selecting other options from the drop down menus.

8. How to download Fragment Analysis .fsa files

a. From the home page, select the underlined number to the right of Folders under the My

Data Dashboard

b. Click on the number in the FSA column associated with the order of interest to view files.

c. Select All Files in the Folder by clicking on the word all. The default is to show only 25.

d. Then select all files by choosing the arrow selection highlight box.

e. Lastly choose from the drop down menu at the bottom of page to download files as .zip file. In the browser being used make sure the path for downloads is known.