Thermo Fisher Scientific MicroSEQ User Manual

MicroSEQ™ ID Software For SeqStudio Genetic Analyzer v1.0

USER GUIDE

for use with the MicroSEQ™ ID family of detection kits

Catalog Numbers A49380 and A49382

Publication Number MAN0019554

Revision A.0

™

For Research Use Only. Not for use in diagnostic procedures.

Life Technologies Corporation | 200 Oyster Point Blvd | South San Francisco, CA 94080 | USA For descriptions of symbols on product labels or product documents, go to thermoﬁsher.com/symbols-deﬁnition.

The information in this guide is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.

Revision history: Pub. No. MAN0019554

Revision Date Description

A.0 14 January 2021 New document for the MicroSEQ™ ID Software For SeqStudio™ Genetic

Analyzer v1.0.

Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept the terms and conditions of all applicable Limited Use Label Licenses.

TRADEMARKS: All trademarks are the property of Thermo Fisher Scientiﬁc and its subsidiaries unless otherwise speciﬁed.

■

CHAPTER 1 Product information .................................................. 7

Product description ............................................................. 7

System vs. Lite ................................................................. 7

Minimum computer requirements ................................................. 8

Compatibility matrix ............................................................. 8

Tutorial data .................................................................... 8

■

CHAPTER 2 Navigate the software .............................................. 11

User groups and privileges ...................................................... 12

Major workﬂows ............................................................... 14

Navigate the software .......................................................... 15

Home screen .............................................................. 15

Options window ........................................................... 16

MicroSeqID Manager window .............................................. 17

New Project Wizard setup screens .......................................... 18

Open Project window ...................................................... 21

SAE Manager ............................................................. 22

Create MicroSEQ ID Run setup screens ..................................... 23

Software toolbars .............................................................. 25

General toolbar ............................................................ 25

Analysis toolbar ........................................................... 26

Display toolbar ............................................................ 26

Naming conventions ............................................................ 27

Set options .................................................................... 27

Set up general defaults ..................................................... 27

Enable Auto ID ............................................................ 29

Customize the display settings ................................................... 30

MicroSEQ

™

ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Contents

■

CHAPTER 3 Use SAE ............................................................ 34

Use the MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer SAE Manager ...... 35

Set up user accounts ...................................................... 35

Set up authentication ...................................................... 38

Set up the audit trail ........................................................ 39

Set up electronic signatures ................................................. 44

Use the SeqStudio™ Genetic Analyzer SAE Administrator Console ................... 48

Default audit and e‑signature settings ........................................ 48

Enable SAE on the SeqStudio™ Genetic Analyzer .............................. 48

Create an SAE user account ................................................ 49

Conﬁgure account setup and security policies ................................. 49

Enable or disable the audit function ......................................... 50

Enable or disable the e‑signature function ................................... 51

CHAPTER 4 Create, run, then evaluate a MicroSEQ ID Run .................. 52

Workﬂow ..................................................................... 52

Create a MicroSEQ ID Run ...................................................... 53

Start the run on the SeqStudio™ Genetic Analyzer .................................. 55

Conﬁrm that the MicroSEQ ID Run has started .................................... 58

Conﬁrm that the run is complete ................................................. 58

View the report ................................................................ 59

Save a MSID Run as a template .................................................. 60

Create a MSID Run from a template .............................................. 61

■

CHAPTER 5 Create and analyze a New Project ................................ 63

Before you begin ............................................................... 64

Create a custom library ..................................................... 64

Create a master analysis protocol ............................................ 68

Create a custom report ..................................................... 75

Change the report settings .................................................. 78

Create a project ................................................................ 79

Select project settings ...................................................... 79

Create a new specimen and import sample ﬁles ............................... 81

View the project setup summary ............................................. 83

Finish and analyze the project data ............................................... 83

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

■

CHAPTER 6 Review the results and generate a report ........................ 85

View the Analysis QC Report .................................................... 85

Interpret the Auto-ID section ................................................ 87

Interpret the specimen analysis section ...................................... 88

View the Library Search Report .................................................. 91

Interpret the Hit List section ................................................. 92

Interpret the Concise Alignment section ...................................... 92

Interpreting the Phylogenetic Tree section ................................... 94

Edit, then reanalyze the project .................................................. 95

When to edit the project .................................................... 95

Edit a consensus sequence ................................................. 95

View the assigned analysis protocol .......................................... 98

Select a dierent analysis protocol ........................................... 99

Reanalyze, then save the project ........................................... 100

Electronically sign your work ................................................... 101

Select an Audit Reason ........................................................ 104

View and verify electronic signatures ............................................ 105

View the Electronic Signature Report ....................................... 105

Verify a project ........................................................... 105

Select reports to export or print ................................................. 106

View the report ........................................................... 106

Export the report ......................................................... 106

Print the report ........................................................... 107

Contents

■

APPENDIX A Troubleshooting .................................................. 108

■

APPENDIX B Create a phylogenetic tree ...................................... 109

Create a phylogenetic tree ..................................................... 109

Search libraries to add sequences to the tree ................................ 109

Search projects to add specimens to tree ................................... 111

Create a phylogenetic tree ................................................. 112

Search for specimens to create new project ................................. 113

■

APPENDIX C Maintenance ...................................................... 114

Maintenance schedule ......................................................... 114

Manage projects .............................................................. 115

Export a project .......................................................... 115

Delete a project .......................................................... 115

Manage SAE ................................................................. 115

Export user accounts ..................................................... 115

Export authentication settings .............................................. 116

Export the Application Level Audit Report .................................. 116

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Contents

■

Archive application audit records ........................................... 117

Restore application audit records ........................................... 117

Backup data ................................................................. 118

Backup the MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer .......... 118

Backup the SeqStudio™ Genetic Analyzer data ............................... 119

Backup SeqStudio™ Genetic Analyzer SAE records ........................... 119

Restore SeqStudio™ Genetic Analyzer SAE records ........................... 120

APPENDIX D Documentation and support .................................... 121

Related documentation ........................................................ 121

Customer and technical support ................................................ 121

Limited product warranty ...................................................... 122

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Product description .................................................................... 7

■

System vs. Lite ........................................................................ 7

■

Minimum computer requirements ........................................................ 8

■

Compatibility matrix ................................................................... 8

■

Tutorial data .......................................................................... 8

■

Product description

The Applied Biosystems™ MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 is part of a streamlined workﬂow for microbial identiﬁcation of bacteria and fungi. MicroSEQ™ chemistry kits are used to generate PCR products that are sequenced on a SeqStudio™ Genetic Analyzer. The MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 compares the sequencing data to validated microbial libraries and generates an identiﬁcation report with percent similarity. The report includes a ﬁnal identiﬁcation list of the organisms that closely match the unknown sample and a phylogenetic tree. Security, audit, and e-signature capabilities are included to help enable 21 CFR Part 11 compliance.

Product information

System vs. Lite

In addition to the System version of MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer, a Lite version is also available for use on a stand-alone PC (not connected to the Genetic Analyzer). Use the Lite version if you plan to perform only the data analyses. Use the System version if you plan to run a complete workﬂow on the SeqStudio™ Genetic Analyzer.

Note: The MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer uses POP–1™ polymer. For more information, see the SeqStudio™ Genetic Analyzer Instrument and Software User Guide (Pub. No. MAN0018646).

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 1 Product information

Minimum computer requirements

The MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer is shipped with a computer. The computer has the following requirements.

Component Requirement

Computer Intel Core i7-8700CPU @3.20 Ghz, with 16GB of RAM and a minimum of 4GB

hard disk space.

Operating system Windows™ 10 IoT; 64‑bit

Compatibility matrix

The MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 is compatible with the following:

•

SeqStudio™ Data Collection Software v1.2.1 and v1.2.3

•

SeqStudio™ Genetic Analyzer ﬁrmware version 1.2.2

•

SeqStudio™ Genetic Analyzer SAE Admin console v2.0

•

MSID libraries

–

MSID 16S rDNA Full Gene Library v2.0

–

MSID Fungal Libray v2018

–

MicroSEQ_ID_16S_rDNA_500_Library_v2019

–

MicroSEQ_ID_16S_rDNA_500_Supplemental_Library_v2019

Tutorial data

The MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 installation contains tutorial data. The tutorial data is in the following installation drive locations.

Table 1 Tutorial data: sample ﬁles

Specimen

MicroSEQ Bacterial 500 (S. aureus)

MicroSEQ Bacterial 500 (B. atropheus)

MicroSEQ Bacterial 500 (M. luteus)

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\Bacterial500Samples\500Saureus

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\Bacterial500Samples\Bacillus atropheus

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\Bacterial500Samples\Bacterial500_Mluteus

Folder name File name and extension

Specimen1_F.ab1

Specimen1_R.ab1

A2_F-

BA_20200709_185023.ab1

B2_R-

BA_20200709_185024.ab1

Specimen1_F_3500xl.ab1

Specimen1_R_3500xl.ab1

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 1 Product information

Table 1 Tutorial data: sample ﬁles (continued)

Specimen Folder name File name and extension

Tutorial data

MicroSEQ Bacterial 500 (C. sporogens)

MicroSEQ Full Gene

(B. cereus)

MicroSEQ Full Gene

(C. sporogens)

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\Bacterial500Samples\Clostridium sporogens

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\BacterialFullGeneSamples\BacterialFullGene_Bcereus

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\BacterialFullGeneSamples\Clostridium Sporogens

E2_F-

CS_20200709_193231.ab1

F2_R-

CS_20200709_193231.ab1

Specimen1_1F_3500.ab1

Specimen1_1R_3500.ab1

Specimen1_2F_3500.ab1

Specimen1_2R_3500.ab1

Specimen1_3F_3500.ab1

Specimen1_3R_3500.ab1

C12_CS2F_20200719_090749.a

D12_CS2R_20200719_090750.

ab1

G10_CS12F_20200717_144743

.ab1

G11_CS3F_20200717_164910.

ab1

MicroSEQ Full Gene

(E. coli)

MicroSEQ Fungal

(A. brasilensis)

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\BacterialFullGeneSamples\Escherchia coli

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\FungalSamples\Aspergillus brasilensis

H10_CS1R_20200717_144744.

ab1

H11_CS3R_20200717_164911.

ab1

A5_EC-1-

F_20200717_031117.ab1

B5_EC-1-

R_20200717_031118.ab1

C5_EC-2-

F_20200717_031119.ab1

D5_EC-2-

R_20200717_031120.ab1

E5_EC-3-

F_20200717_041203.ab1

F5_EC-3-

R_20200717_041204.ab1

C3_R-

AB_20200401_200628.ab1

D3_F-

AB_20200401_200629.ab1

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 1 Product information

Tutorial data

Table 1 Tutorial data: sample ﬁles (continued)

Specimen Folder name File name and extension

MicroSEQ Fungal

(S. cerevisiae)

MicroSEQ Fungal

(Positive control)

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\FungalSamples\Fungal_Scerevisiae

Drive letter:\AppliedBiosystems\MicroSeqID\Tutorial Data\FungalSamples\Positive control

Specimen1_F_3500xl.ab1

Specimen1_R_3500xl.ab1

C1_F-

PC_20200709_182305.ab1

D1_R-

PC_20200709_182306.ab1

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Navigate the software

■

User groups and privileges ............................................................ 12

■

Major workﬂows ...................................................................... 14

■

Navigate the software ................................................................. 15

■

Software toolbars .................................................................... 25

■

Naming conventions .................................................................. 27

■

Set options .......................................................................... 27

■

Customize the display settings ......................................................... 30

■

The installation of the MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer and the SAE Administrator Console v2.0 for use with the SeqStudio™ Genetic Analyzer is performed by a ﬁeld service engineer. The installation uses a direct connection between the SeqStudio™ Genetic Analyzer and the computer housing the software (Cloud services are not supported). Both the MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer and the SAE Administrator Console v2.0 require a user login process. Logging in with a user name allows the software to track each user’s interactions with the software.

The ﬁrst user created is automatically assigned Administrator privileges.

Start the MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer by double-clicking the MicroSEQ ID icon

The Log In dialog box opens, showing the last user’s username.

on the desktop.

™

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 2 Navigate the software

User groups and privileges

Enter your user name and password, then click OK.

User groups and privileges

Three user groups are deﬁned in the software: Administrator, Scientist, and Analyst. Each of these user groups has the privileges listed in the table below.

User Group Privileges

Administrator All Scientist and Analyst privileges, plus:

•

Set up Auto-ID parameters

•

Set up users

•

Set up authentication settings

•

Set up auditing trail

•

View, archive, and restore application level audit records

•

Set up electronic signatures

Scientist All Analyst privileges, plus:

•

Set up general defaults

•

Create libraries

•

Create analysis protocols

•

Set up custom reports

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

(continued)

Analyst

Chapter 2 Navigate the software

User Group Privileges

•

Create MicroSEQ ID runs and run templates

•

Conﬁrm Run Start

•

Conﬁrm Run Complete

•

Export Plate

•

Access to View Analysis Progress

•

Create a project

•

Analyze the project

•

Evaluate the results

•

Export projects

•

Import projects

•

Add a specimen to the project

•

Add samples to the project

•

Electronically sign your work

•

Select the report format

•

Export or print reports

•

View Auto-ID parameters (if Auto-ID enabled)

User groups and privileges

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 2 Navigate the software

Major workﬂows

“Conﬁrm that the MicroSEQ ID Run has started”

“Conﬁrm that the run is complete” on page 58 “Finish and analyze the project data” on

Create a MicroSEQ ID Run

“Create a MicroSEQ ID Run” on page 53 “Create a master analysis protocol” on

▼ ▼

“Start the run on the SeqStudio™ Genetic

Analyzer” on page 55

▼ ▼

on page 58

▼ ▼

“View the report” on page 59 “View the Analysis QC Report” on page 85

▼ ▼

“Create a custom report” on page 75

and “View the Library Search Report” on

Create a New Project

page 68

“Create a project” on page 79

page 83

page 91

“Select reports to export or print” on page 106

(Optional) “Edit, then reanalyze the project” on

page 95

▼

“Select reports to export or print” on page 106

or “Export a project” on page 115

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Navigate the software

4 5 6

Home screen

Use the home screen to:

•

Create and open MicroSEQ ID runs and templates

•

Create, open, and analyze projects

•

Display the Project View, Specimen View, or Sample View

•

Display the Report Manager to display library search results and other reports

•

Set default display settings that are saved with your user account

•

Change your password

•

Access the MicroSEQ ID Manager to manage MicroSEQ ID runs and templates, projects, libraries, analysis protocols, and custom reports

•

Access the Options dialog box via the Tools menu, to view or set Auto-ID and general system settings

•

Access the SAE Manager to manage security, audit, and electronic signature functions (Administrators only)

Chapter 2 Navigate the software

Navigate the software

New Project

Open Project

SAE Manager

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Create MicroSEQ ID Run Open MicroSEQ ID Run Open MicroSEQ ID Template

Chapter 2 Navigate the software

Navigate the software

Options window

Note: Access the Options window by clicking Tools ► Options.

Use the Options dialog box to:

•

Set the export and report defaults for the current user (Scientist and Administrator only).

•

Enable or disable Auto-ID for all projects and edit Auto-ID settings for MicroSEQ™ ID kits (Administrator only).

General tab

Auto-ID tab

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

MicroSeqID Manager window

32 4 5

Use the MicroSeqID Manager window to enter and manage the information necessary to perform analyses on your projects:

•

Open, edit, copy, delete, import, and export projects

•

Create, open, copy, and delete MicroSEQ ID Runs and MicroSEQ ID Run templates

•

Create, edit, copy, delete, import, and export custom libraries, analysis protocols, custom reports

Chapter 2 Navigate the software

Navigate the software

Projects tab

Libraries tab

Analysis Protocols tab

Custom Reports tab

MicroSEQ ID Runs tab

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 2 Navigate the software

Navigate the software

New Project Wizard setup screens

Use the New Project Wizard to create projects.

Select Project Settings screen

Use this screen to enter the following parameters.

•

Project Name

•

Number of Matches to Display

•

Kit used

•

Project Analysis Protocol

•

Project Analysis Report

•

Select the library or libraries to use

Project Name

Matches to Display

Kit

Project Analysis Protocol

Project Analysis Report

Select Library to use

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Create Specimens screen

Use this screen to add your samples or new specimens.

Chapter 2 Navigate the software

Navigate the software

Double-click the name to edit if needed

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 2 Navigate the software

Navigate the software

Finish screen

Use this screen to Finish or Finish and Analyze your new project.

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Open Project window

Note: Access the Project window by clicking Open Project on the home screen or by clicking

File4Open Project, then selecting an existing project.

Use the Project window to select a project to open. Once the project is open, you can:

•

Import specimens/sample ﬁles

•

Adjust project analysis parameters using the Properties and Settings of the Project or Specimen

•

View, export, or print project data (Project Navigator, Specimen View, or Sample View)

•

Access the Analysis Protocol Viewer to view analysis information

•

Access the Report Manager to select a report, view, export, or print project analysis reports

Chapter 2 Navigate the software

Navigate the software

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 2 Navigate the software

Navigate the software

SAE Manager

Use the SAE Manager to manage the security, audit, and electronic signature (SAE) features for users and projects.

User tab

Authentication tab

Audit Trail tab

Electronic Signature tab

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Create MicroSEQ ID Run setup screens

Use the Create MicroSEQ ID Run setup screens to enter the run and Project information and to conﬁrm the run properties.

Project Setup screen

Use this screen to enter the following parameters:

•

MicroSEQ ID Run Name

•

Run Module

•

Select the Project Analysis Report

•

Number of Matches to Display

•

Add Projects and enter Project names

•

Enter the number of Specimens

•

Select the MicroSEQ ID kit being used for each project

•

Select the library or libraries to use for analysis

Chapter 2 Navigate the software

Navigate the software

MicroSEQ ID Run Name

Run Module

Project Analysis Report

Matches To Display

Add Project

Project Name

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 2

Navigate the software

Specimen Setup screen

Use this screen to edit specimen names if needed.

Plate Layout screen

Use this screen to determine the plate layout or to print your plate setup.

Analysis Progress screen

Use this screen to:

•

Conﬁrm Run Complete (on the SeqStudio™ Genetic Analyzer)

•

Cancel Run (on the SeqStudio™ Genetic Analyzer)

•

Open Report

•

View Specimen data

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

1 2 3

Open Report

1 2 3 4 5 6 7 8 9 10 11

Cancel Run

Conﬁrm Run Complete

Chapter 2 Navigate the software

Software toolbars

The MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 toolbars display buttons for commonly used software functions. The following diagrams detail the names and descriptions for each button.

General toolbar

The General toolbar contains general processing tools for creating projects.

New Project

Open Project

Save Project

MicroSEQ ID Manager

New Specimen

Import Samples To Project

Find

Find Again

Undo Base Change

Delete

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

1 2 3 4 5 6 7

1 2 3 4 5 6 7 8 9 10 11 12

Chapter 2 Navigate the software

Software toolbars

Analysis toolbar

The Analysis toolbar contains project analysis tools.

Analyze Samples (Green when available)

Analysis Protocol Viewer

Report Manager

Copy Entire Sequence

BLAST button. Link to NCBI's BLAST search tool

Electronic Signature

MicroSEQ ID Product Information

Help (link to PDF of this guide)

The BLAST® button links you to the National Center for Biotechnology Information (NCBI) website that maintains the Basic Local Alignment Search Tool (BLAST®) tool.

Display toolbar

The Display toolbar contains viewing options for the projects.

Display Settings

Show/Hide Electropherogram

Show/Hide All Electropherogram

Full View of Electropherogram

Zoom In

Zoom Out

Show/Hide Consensus QV

Show/Hide Sample QV

View Column Selector

Inverse View

View Original Sequence

View Aligned EP

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Naming conventions

The following characters are not allowed in the MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer:

Table 2 Create MicroSEQ ID Run workﬂow

Software ﬁeld Characters not allowed

MicroSEQ ID Run Name \ / : * ? " < > | , space ~ ` ^ ‘

Project Name \ / : * ? " < > | , space ~ ` ^ ‘

Specimen Name \ / : * ? " < > | , space ~ ` ^ ‘ _

Table 3 New Project workﬂow

Software ﬁeld Characters not allowed

Project Name \ / : * ? " < > | , space

Chapter 2

Navigate the software

Naming conventions

Specimen Name \ / : * ? " < > | , space

Note: User Names (created in SAE Manager) allow only alphanumeric characters (A-Z / a-z / 0-9) with no spaces.

An error message is displayed if a space or any of these characters is used. You must remove the invalid character to continue.

Set options

The Options dialog box is used to:

•

Set the export and report defaults

•

Enable or disable Auto-ID for project analysis and edit Auto-ID settings for MicroSEQ™ ID kits.

Set up general defaults

IMPORTANT! You must have Administrator or Scientist privileges to perform this procedure.

For convenience, you can set up the general defaults to:

•

Display and/or export reports after analysis

•

Specify a directory to which reports are automatically exported

Note: If you do not specify a directory, the default directory opens to C:\.

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 2 Navigate the software

Set options

In the MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 home screen, select Tools4Options to open the Options dialog box.

In the General tab, select the Display Reports after Analysis check box.

The default replacement character is a hyphen (-)

Review and update the export settings in the General tab as needed.

Note: The settings in this tab apply to the current user only.

Click OK to save your defaults.

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Enable Auto ID

The Auto-ID state cannot be changed while projects are open. Close any open projects.

IMPORTANT! You must have Administrator privileges to perform this procedure. Scientists and

Analysts can view only.

In the home screen, select Tools4Options4Auto-ID.

In the Options dialog box, enter the required settings.

Chapter 2

Navigate the software

Set options

Parameter Description

Turn Auto-ID On or O Select Auto-ID On to enable specimen

identiﬁcation from a library during data analysis.

Kits Select the appropriate kit to apply Auto-ID

settings during project analysis. To edit the parameters, click Edit Auto-ID

Parameters. Enter the new Auto-ID specimen requirements and thresholds for the selected kits, then click OK to save.

Click OK.

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

Chapter 2 Navigate the software

Customize the display settings

Display settings control how projects are visually displayed when they are ﬁrst opened after analysis is complete. Each user can customize his or her own display settings.

To customize the display settings:

Open a project or create a project to enable display settings.

In the MicroSeq ID Analysis home screen, select Analysis > Display Settings or click the Display Settings icon in the Display toolbar to open the Display Settings window.

Select the General tab.

In the Comments ﬁeld, type My display settings.

MicroSEQ™ ID Software For SeqStudio™ Genetic Analyzer v1.0 User Guide

+ 93 hidden pages