Roche 05434564001 Sequencing Solutions Signal Map User manual

Brand: Roche

Model: 05434564001 Sequencing Solutions Signal Map

Category: Graphics software

Type: User manual

SignalMap v2.0.0 Software User’s Guide

Version 3.2

For Research Use Only.

Not for use in diagnostic procedures.

SignalMap v2.0.0 Software User’s Guide, v3.2

Edition

Version 1.0, Dec 2006. Version 2.0, March 2013. Version 3.0, January 2014. Version 3.1, September 2018. Version 3.2, May 2019.

Service Marks and Trademarks

All other product names and trademarks are the property of their respective owners.

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typographical, technical or other inaccuracies in this document. Roche reserves the right to periodically change information that

is contained in this document; however, Roche makes no commitment to provide any such changes, updates, enhancements or

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You are responsible for understanding and using the software described within. Roche does not guarantee any results you

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SignalMap v2.0.0Software User’s Guide, v3.2

Table of Contents

Preface ........................................................................................................................................... 5

Intended Use ................................................................................................................................................. 5

Contact Information .................................................................................................................................... 5

Technical Support............................................................................................................................... 5

Conventions Used in This Guide ........................................................................................................... 5

Symbols ................................................................................................................................................... 5

Text ........................................................................................................................................................... 5

Chapter 1. Before You Begin.................................................................................................... 6

What is SignalMap Software? ................................................................................................................ 6

Recommended System Requirements ................................................................................................ 6

Installing SignalMap Software ............................................................................................................... 6

Checking for Updates ................................................................................................................................ 7

Chapter 2. Understanding Basic Concepts .......................................................................... 8

SignalMap Workflow .................................................................................................................................. 8

Navigating the SignalMap Software Interface ................................................................................ 8

Toolbar .................................................................................................................................................... 9

Panes and Pane Selector ................................................................................................................. 9

Information and Attributes ............................................................................................................ 10

Position Scale ..................................................................................................................................... 11

Tracks .................................................................................................................................................... 11

Status Bar ............................................................................................................................................. 12

Printing Data ................................................................................................................................................ 12

Viewing or Changing Print Settings .......................................................................................... 12

Previewing Data Before Printing ................................................................................................ 13

Printing Data as Shown on the Screen .................................................................................... 13

Chapter 3. Importing Data ...................................................................................................... 14

Recognized File Types ............................................................................................................................. 14

GFF Files ............................................................................................................................................... 14

BED Files .............................................................................................................................................. 14

Importing Data ............................................................................................................................................ 14

Annotation .................................................................................................................................................... 15

Hyperlinks ..................................................................................................................................................... 16

Chapter 4. Browsing Data ....................................................................................................... 18

Viewing Panes and Tracks ..................................................................................................................... 18

Viewing Tracks on a Particular Pane ........................................................................................ 19

Viewing All Tracks ............................................................................................................................ 19

Going To a Specific Location ....................................................................................................... 20

Reorganizing Panes .................................................................................................................................. 20

Reordering Panes ............................................................................................................................. 20

Deleting Panes ................................................................................................................................... 20

Reorganizing Tracks ................................................................................................................................. 21

Selecting Tracks ................................................................................................................................ 21

Moving Tracks.................................................................................................................................... 21

SignalMap v2.0.0 Software User’s Guide, v3.2

Deleting Tracks .................................................................................................................................. 21

Searching ...................................................................................................................................................... 22

Magnifying Regions of Data ................................................................................................................. 22

Zooming In (Increasing Magnification)................................................................................... 23

Zooming Out (Decreasing Magnification) ............................................................................. 24

Changing the Track Height ................................................................................................................... 24

Changing the Y Axis ................................................................................................................................. 25

Manually Setting the Y-Axis Scale ............................................................................................ 25

Automatically Setting the Y-Axis Scale ................................................................................... 25

Changing the Track Style ....................................................................................................................... 25

Changing the Track Color ...................................................................................................................... 26

Highlighting Tracks ................................................................................................................................... 27

Selecting a Cursor Track ............................................................................................................... 27

Highlighting a Data Point .............................................................................................................. 27

Jumping to the Next or Previous Data Point ......................................................................... 28

Using Hyperlinks ........................................................................................................................................ 28

Chapter 5. Exporting Data ....................................................................................................... 30

Selecting Data ............................................................................................................................................. 30

Selecting One Region ..................................................................................................................... 30

Selecting Multiple Regions ........................................................................................................... 30

Exporting Selections to a GFF File ...................................................................................................... 31

Exporting a Screen Capture .................................................................................................................. 31

Exporting a Screen Capture as a Windows Metafile ......................................................... 32

Exporting a Screen Capture as a BMP, GIF, PNG or TIFF ................................................ 32

Appendix A. GFF Files ............................................................................................................... 34

Understanding GFF Files ........................................................................................................................ 34

Examples in Text File Format ................................................................................................................ 35

Appendix B. BED Files .............................................................................................................. 36

Understanding BED Files ....................................................................................................................... 36

SignalMap v2.0.0 Software User’s Guide, v3.2

Preface

Intended Use

The SignalMap software is intended for research use only. Not for use in diagnostic

procedures.

The SignalMap software is a visualization tool for Roche design data.

Contact Information

Technical Support

If you have technical questions, contact your local Roche Technical Support. Go to

www.roche.com/support for contact information.

Conventions Used in This Guide

Symbols

Symbol Description

Important Note. Information critical to the success of the procedure or use of the product. Failure

to follow these instructions could result in compromised data.

Information Note: Designates a note that provides additional information concerning the current

topic or procedure.

Text

Conventions Description

Numbered listing

Indicates steps in a procedure that must be performed in the order listed.

Italic type, blue

Identifies a resource in a different area of this manual or on a web site.

Italic type

Identifies the names of dialog boxes, windows, tabs, panels, views, or message

boxes in the software.

Bold type

Identifies names of menus and controls (buttons, checkboxes, etc.) in the

software.

SignalMap v2.0.0 Software User’s Guide, v3.2

Chapter 1. Before You Begin

What is SignalMap Software?

The SignalMap software enables you to visualize Roche design data. It provides the ability to:

• Import one or more GFF (General Feature Format) or BED files.

• Visualize tracks of data organized into panes and tracks.

• Link to a web site with detailed information for a selected gene.

• Export a subset of your data.

• Print and export screen captures.

Recommended System Requirements

Specification

Memory 512 MB

Processor Pentium III 600 MHz or equivalent

Hard Drive Disk 10 MB

Operating System Microsoft Windows XP, Windows 7

Monitor SXGA 1280x1024 with 16-bit colors

Hardware Graphics Driver Recommended

Keyboard Standard

Software Java 6

Installing SignalMap Software

You must install the SignalMap software from files downloaded from the Roche website at

https://sequencing.roche.com/en/products-solutions/by-category/target-

enrichment/software/signal-map-software.html.

1. Click on the Download link.

2. Select Open to run the installer or Save to save the installer file to your computer.

3. Unzip the downloaded file.

4. Double-click SignalMap_install.exe.

5. Follow the on-screen installer instructions (Figure 1).

By installing the SignalMap software, you agree to the terms and conditions of the relevant

software license agreement(s).

Chapter 1. Before You Begin

SignalMap v2.0.0 Software User’s Guide, v3.2

Figure 1: SignalMap Installer

Checking for Updates

To verify that you are using the most up-to-date version of this guide to view your designs, go

to https://sequencing.roche.com/en/products-solutions/by-category/target-

enrichment/software/signal-map-software.html

SignalMap v2.0.0 Software User’s Guide, v3.2

Chapter 2. Understanding Basic

Concepts

This chapter describes the basic concepts underlying the software to enable you to use

SignalMap software effectively and efficiently.

SignalMap Workflow

The following is a broad overview of a typical session using SignalMap software:

1. Start the SignalMap software. The SignalMap program window appears.

2. Choose File -> New to create a new document window.

3. Import your data files. For more information, see the Importing Data section in Chapter

3. Importing Data.

4. Explore your data.

- Browse your data. For more information, see the

Viewing Panes and Tracks

section in

Chapter 4. Browsing Data.

- Export your data or screen capture. For more information, see the Exporting Your

Data section in Chapter 5. Exporting Data.

- Print a screen. For more information, see the Printing Data section in this chapter.

Navigating the SignalMap Software Interface

When you import files into SignalMap software, a navigation window similar to Figure 2

appears:

Figure 2. SignalMap software Navigation Window

Chapter 2. Understanding Basic Concepts

SignalMap v2.0.0 Software User’s Guide, v3.2

Toolbar

Use the buttons on the toolbar to quickly access SignalMap features. A description of each

icon is provided in Table 1 below.

You can display or hide the toolbar by choosing View -> Toolbar.

You can move the pane selector by dragging it with the mouse.

Icon Name Description

Create a New

Document

Creates a new document (or window) in which to import data. The first new

document window is called GFF1. Subsequent windows opened in the same

session are named sequentially, GFF2, GFF3, and so on.

Import Files

Imports existing GFF/BED files, saved with either .gff, .bed, or .txt filename

extension. You can import several files at a time.

Print Preview Displays a preview of the current display before you print.

Print Prints the current display to the selected printer.

Pointer Click to select data or genes.

For locations on the gene track annotated with web addresses, double-click to

activate the hyperlink.

Magnifier Use to zoom in or out of the display in the selected pane. Be aware your

magnification selections will not affect other panes.

• Click in the display to double the magnification around the center of

the click.

• Press the Ctrl key then click to halve the magnification.

• Click and drag to magnify an area.

Ruler Click and drag within a pane to display the Width and Position of the selection in

the header, when the header is displayed.

Autoscale Enables the automatic scaling of the y axis for the selected tracks.

Manual Scale Displays the Manual Scale dialog box, from which you can change the minimum

and maximum y-axis scale for the selected tracks.

Increase

Point Size

Increases the height of the data to make it more visible.

Decrease

Point Size

Decreases the height of the data.

Table 1. Icon Names and Descriptions

Panes and Pane Selector

SignalMap software displays the data from a GFF or BED file in panes. Each pane contains

information corresponding to one seqname defined in the imported file. Typically, a seqname

will be the chromosome or region name for Roche-supplied data.

You can select individual panes from the selection box in the pane selector. Choosing the All

Tracks button displays all tracks.

SignalMap software replaces an empty seqname with a space.

Chapter 2. Understanding Basic Concepts

SignalMap v2.0.0 Software User’s Guide, v3.2

Icon Name Description

Back (Pane

History)

Displays the previous pane in your browsing history.

Forward

(Pane

History)

Displays the next pane in your browsing history.

Information and Attributes

SignalMap software can optionally display information about the dataset and the attributes of

features.

Display Header

Displays the enabled information and attributes, and the Roche logo at the top of the pane.

You can display or hide the header by choosing View -> Display Header.

Loaded Files

Displays information about loaded files:

• Files: An alphanumeric listing of all loaded files.

• Load Time: The total time it took to import data from all files.

You can display or hide the loaded files information by choosing View -> Loaded Files.

Track Statistics

Displays statistics about tracks:

• Rows loaded: The total number of rows from all of the tracks in all of the loaded files.

• Positions Displayed: The exact range of positions currently displayed.

• Total Positions: The exact range of positions from all of the tracks in the pane.

You can display or hide the track statistics by choosing View -> Track Statistics.

Pointer Info

Displays information that corresponds to the feature under the pointer:

• Score: The score for the feature.

• Pos: The first and last position of the feature.

• Attr: The contents of an optional column in a GFF file. Attribute information could

include web site links and annotation.

You can display or hide the pointer info by choosing View -> Pointer Info.

Pointer info is not displayed if there is no feature under the pointer.

Chapter 2. Understanding Basic Concepts

SignalMap v2.0.0 Software User’s Guide, v3.2

Cursor Info

Displays information that corresponds to the feature highlighted by the cursor:

• Score: The score for the feature.

• Pos: The first and last position for the feature.

• Attr: The contents of an optional column in a GFF file. Attribute information could

include web site links and annotation.

You can display the cursor info by choosing Cursor -> Attach Cursor.

You can hide the cursor info by choosing Cursor -> Detach Cursor.

Selection Info

Displays information that corresponds to the selected region:

• Width: The width of the region.

• Position: The first and last position of the region.

The selection info is displayed when either the pointer or the ruler is selected

in the Toolbar.

Select a region by clicking in the pane and dragging the mouse.

Position Scale

Displays the x-axis scale for all tracks in the pane. This scale corresponds to the start and end

column in the GFF file.

Tracks

Figure 3: Tracks

Chapter 2. Understanding Basic Concepts

SignalMap v2.0.0 Software User’s Guide, v3.2

Each track displays data for different types of features in the imported file (Figure 3).

• Y-Axis Scale: Displays the y-axis scale information.

• Track Information: Displays the feature, number of rows, and other information

about the track.

• Highlighted Gene: A transparent gray bar is displayed over the track at the location of

the selected gene.

Status Bar

The status of various lock keys is displayed in the lower right corner of the screen, to the right

hand side of the status bar.

• Caps Lock: Displays CAPS when the Caps Lock key is set on your keyboard.

• Num Lock: Displays NUM when the Num Lock key is set on your keyboard.

• Scroll Lock: Displays SCRL when the Scroll Lock key is set on your keyboard.

Printing Data

SignalMap software prints your data based on the magnification of the display. That is, the

Print command prints exactly what you see on your screen. Therefore, zoom in to the region

before using the Print command. (See the Magnifying Regions of Data section in Chapter 4.

Browsing Data for details.) Data always print to a single page.

Before you print your data, check your print settings. You may need to change the

print orientation from portrait to landscape.

Viewing or Changing Print Settings

1. Choose File -> Print Setup.

 The Print Setup dialog box appears.

2. Select your printer and print properties.

 For example, you may want to change the orientation from portrait to landscape.

3. Click OK to print.

 Your data prints onto one page.

Chapter 2. Understanding Basic Concepts

SignalMap v2.0.0 Software User’s Guide, v3.2

Previewing Data Before Printing

1. Choose File -> Print Preview or click the Print Preview button on the toolbar.

 A preview of what will print displays in the window, as shown in Figure 4.

2. Click Print… at the top of the preview window to print the data.

Figure 4: Print Preview

Printing Data as Shown on the Screen

1. Choose File -> Print or click the Print button on the toolbar.

 The Print dialog box appears.

2. Select your printing preferences.

3. Click OK.

 Your data prints onto one page.

Notes

SignalMap v2.0.0 Software User’s Guide, v3.2

Chapter 3. Importing Data

SignalMap software organizes imported data by seqname, one per pane, then by feature, one

per track, and then by position. This chapter describes the process to:

• Import data

• Import annotation

• Include hyperlinks

Although SignalMap software easily imports very large files (hundreds of

megabytes), it requires significant amounts of memory to do so. Roche

recommends you close other memory-intensive software, such as graphics

programs, when working with SignalMap software to avoid losing information

should those programs stop responding. If SignalMap software stops responding,

try splitting large files by chromosome or region into two or more files and import

those into SignalMap software. If SignalMap software continues to be unresponsive,

report the problem to Roche.

Recognized File Types

GFF Files

The SignalMap software can import and export GFF files with either GFF or TXT filename

extensions. For more information about GFF files, see -

www.sanger.ac.uk/resources/software/gff/spec.html or see the

Understanding GFF Files

section in

Appendix A. GFF Files

BED Files

The SignalMap software can import BED files with either BED or TXT filename extensions.

For more information about BED files, see genome.ucsc.edu/FAQ/FAQformat.html#format1 or

see the

Understanding BED Files

section in

Appendix B. BED Files

Importing Data

You can import any GFF file with a GFF or TXT filename extension, or any BED file with a

BED or TXT filename extension, into SignalMap software.

1. Choose between the following:

- To import data into your current document, choose File -> Import or click the

Import Files button on the toolbar.

- To import data into a new document, choose File -> New or click the New button on

the toolbar.

 A new document window opens, and the Import Files dialog box appears.

Drag and drop GFF/BED files into the current document to import them.

Chapter 3. Importing Data

SignalMap v2.0.0 Software User’s Guide, v3.2

2. Select the files to import. Hold down the Ctrl key while clicking to select multiple files.

3. Click Open.

 The SignalMap software imports the files into the document.

The Import Files window (Figure 5) provides status information that shows the progress of the

import. In this example, SignalMap software has loaded 31% of the third file, representing

46% progress towards the time required to import all files.

Figure 5: Import Files Window

Figure 6 shows an example of data-only GFF files.

Figure 6: Data-Only GFF Files

Each data track imported is assigned to a unique color unless a color is specified as an

attribute of a feature.

BED files without a trackname header, will be placed in tracks named the same as the

filename, with the filename extension removed.

Annotation

The SignalMap software imports annotation (any feature other than data) in the same way as

any other GFF file.

The SignalMap software can display certain tracks with specific colors to enable you to more

easily identify them in the pane. This is achieved by defining the color of each data point or

annotation feature in the attribute column of the GFF file using the color tag (see the

Understanding GFF Files section in Appendix A. GFF Files). Table 2 shows acceptable color

tags.

Chapter 3. Importing Data

SignalMap v2.0.0 Software User’s Guide, v3.2

chr21 hg19_snp137Common snp 33031974 33031974 1

. color 00FFFF; snp_id "rs7277748";

chr21 hg19_snp137Common snp 33032287 33032287

. color=FF0000; snp_id "rs17881180"

Table 2: Acceptable Color Tags

Figure 7 shows a typical example of the use of color tags.

Figure 7: Colored Tracks

Example track color assignments for annotation:

• gene: This track contains information about the start and end of genes. You can click

a gene to highlight all data in the same position as that gene. If web hyperlinks were

specified in the GFF file, you can double-click their location on the gene track to

open your computer’s default web browser and access the specified web site.

Displays with a blue color in Figure 7.

• exon: This track contains exon data. Displays with a brown color in Figure 7.

• data: This track contains user data. Displays with a green color in Figure 7.

Hyperlinks

The SignalMap software treats any http hyperlink in the GFF file’s attribute field as a

hyperlink. URLs can also be specified using the GFF3 tag format url=someurl. You can

separate multiple items in the attribute field with a semicolon (;).

Placing the pointer over a data point containing a hyperlink allows you to view the web

address. Double-clicking data with a hyperlink opens your computer’s default web browser

and accesses the specified web site.

A common use for hyperlinks is to link to web site information about specific genes. This

would be accomplished by adding URL links in the attribute fields for gene feature records.

Table 3 provides acceptable hyperlinks.

chr 1 NGS track1 20 30 30.0 . . chr info; http://www.roche.com

chr1 NGS track1 30 40 40.0 . . url='http://www.roche.com'

chrX NGS track1 10 15 20.0 . . http://www.ncbi.nlm.nih.gov/gene/?term=NM_001412

Table 3: Acceptable Hyperlinks

Chapter 3. Importing Data

SignalMap v2.0.0 Software User’s Guide, v3.2

Notes

SignalMap v2.0.0 Software User’s Guide, v3.2

Chapter 4. Browsing Data

The SignalMap software allows you to quickly browse your GFF (General Feature Format) or

BED data. In this chapter, you learn to:

• View panes and tracks

• Reorganize tracks

• Search data

• Magnify regions of data

• Change the track height

• Change the y-axis scale

• Change the track style

• Change the color

• Highlight track data

• Use hyperlinks

Viewing Panes and Tracks

The SignalMap software organizes data into panes and tracks. Each SignalMap document can

contain up to 32,768 panes.

Each pane can contain an unlimited number of tracks. A pane contains data tracks

corresponding to one seqname. Roche-supplied data will usually be organized to display one

chromosome or region per pane. The name of the pane (seqname) appears above the first

track selected, as shown in Figure 8.

Typically, each individual track contains only one data or annotation feature. The feature

name and other details are printed below the graphical representation of the data on the track.

When a new file is imported, the first pane is selected by default.

Chapter 4. Browsing Data

SignalMap v2.0.0 Software User’s Guide, v3.2

Viewing Tracks on a Particular Pane

1. Use the pane selector to select to a pane of interest or browse through panes using the

history buttons and the up/down buttons.

2. The SignalMap software displays the data tracks for the selected pane (seqname), as

shown in Figure 8.

Figure 8: Tracks on a Selected Pane

Viewing All Tracks

1. Select All Tracks (the top selection in the pane selector drop-down list).

 All tracks appear in the All Tracks pane, as shown in Figure 9.

Figure 9: All Tracks Pane

Chapter 4. Browsing Data

SignalMap v2.0.0 Software User’s Guide, v3.2

2. The tracks for each seqname appear with alternating color backgrounds (white and lime

green) to separate the seqname data visually.

3. Use the window’s vertical scroll bar keys to scroll to the tracks to view in this pane.

Going To a Specific Location

1. Choose View -> Go to Position or press Ctrl + G.

 The Go to Position dialog box appears (Figure 10), displaying the current pane and its

Start and End Positions.

Figure 10: Go To Position Dialog Box

2. Select the pane edit the position, and click OK.

 The SignalMap software displays the pane and positions selected.

Reorganizing Panes

The SignalMap software sorts newly imported panes in the order that they were in the file.

You can change the sort preference in the Pane menu. You can also delete panes you do not

want.

Reordering Panes

1. Choose Pane -> Sort.

2. Choose from the following options:

- Unsorted: Panes are displayed in the order they were loaded.

- Alphanumeric: Panes are sorted alphabetically (case-insensitive). If the pane starts

with “chr”, the pane is sorted numerically using the number following “chr”.

Deleting Panes

1. Select the pane to delete.

2. Choose Pane -> Delete.

 The SignalMap software deletes the pane.

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Roche 05434564001 Sequencing Solutions Signal Map User manual

Brand: Roche

Model: 05434564001 Sequencing Solutions Signal Map

Category: Graphics software

Type: User manual

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