Operating system: MagicViewer is designed to run on multi-platform, including Windows, Linux and Mac et al.
Java version: MagicViewer is written in Java programming language and needs a recent version of Java (JRE version 1.6.0 or higher).
Overview introduction of the main page contents
MagicViewer main page
Compact alignments
In multiple sequence alignment space, users can have a graphic view of millions of short reads mapped to the reference genomes. It supports configure display of integrated sequence alignments in any scale desired and highlights with definable color and font scheme to suit their needs. Move the mouse over a point, users will get a tooltip of auxiliary information, such as reads ID, location, base quality, read length and orientation.
Read coverage
In the top of graphical representation of short reads alignments, users can visualize the sequencing depth distribution of mapped reads along the reference sequence.
SNP Image
We use vertical line to show the SNP information embedded in DNA sequence. Each line is positioned according to the location of the SNP it represents. The line height represents the SNP score for the SNP at that position. The SNP score is the number of sequences containing the SNP at that position. The colour of a line represents the SNP type. When the mouse is held over a line, users can get more detailed information about that SNP. Double click SNP image provides a way to navigate to specific location by coordinates to facilitate the retrieval of SNP annotations.
File Menu
New project – for fist time use, click new project to provide a reference file in fasta format, a alignment file in bam format and annotation files in gff, bed, vcf format. Click “display” button, loading file process will finish in a few seconds. Then the main page displayed as above.
Load - quickly opens an existing project saved as a log file
Save - save current record when you finish working on it
Save as - allows you to choose a new name, directory to save the document
Import - add annotation files
Export - lead out as an image in PDF format
Close - shut down current project
Quit - exits the application
View Menu
Showing annotation: options for showing annotation
Showing Coverage: options for showing coverage
Showing Reference: options for showing reference
Showing Alignment: options for showing alignment
New window: a new, blank document appears on the screen
Analysis Menu
Variation Calling
Variation Filtration
Variation Annotation
Primer Design
Settings Menu
Annotation parameters: provide user-defined parameters highly configurable allowing users to define view mode, arrow mode, read height, color, vertical space, change track display height and background color.
Annotation tracks: functions for reordering of track location and add/delete related tracks.
Alignment parameters: users can change font and colors in many different combinations, such as each base and background color. Zooming can be performed by choosing from the settings menu or using toolbar buttons "+" and
"-".
Toolbars
Several basic items can be found on the toolbars. You can use these tool bars for zooming in/out, selecting current contigs or coordinate settings etc.
In addition, a step by step documentation for the test data application will come soon!
