User interface

This page introduces the different components of GenomeView and explains a number of naming conventions we use throughout the documentation.

Components of GenomeView
The GenomeView GUI is divided into two columns. The left side is a graphical representation of the data, while on the right side you can find additional information, controllers and options in the form of tables.

Visual description of the user interface (click to enlarge)Visual description of the user interface (click to enlarge)

Tracks

All visualizations in GenomeView are organized into tracks. A track typically holds on particular type of data or one particular data set. There can be multiple tracks of each type.
When loading new data, a new track is added.

On the right side of the window there is an overview of all tracks that are currently available.

You can reorder the tracks by dragging them up and down in this table, hide them by clicking the eye icon or remove them with the garbage bin icon.

Gene structure

Gene structure track

Gene structure track (click to enlarge)Gene structure track (click to enlarge)

This tracks shows a number of things, some of which only are visible when you are sufficiently zoomed in.
Things to know about this track:

  • This track is divided into two by a ruler which indicates the current genomic location.
  • Within this track, everything above the ruler is on the forward strand, anything below the ruler is on the reverse strand
  • Both the forward strand part and the reverse strand part have a nucleotide band and 3 possible translation frame bands.
  • In the default configuration, potential donor and acceptor sites will be painted in yellow and blue on the nucleotide band.
  • The six reading frames have potential start and stop codons indicated in green and red.
  • The light blue rectangles visualizes the structure of a gene in terms of strand and the phase of each exon.

Feature track

The feature track can display a multitude of annotation information, supplied as GFF or BED files. Features like CDS, RNA, SNP, etc... are displayed as rectangles in different colors. A triangle on one side can indicate the strand. When zoomed in enough, feature names are displayed when available.

The labels on each of the features are encoded in the input file. The track will look for the following keys to find a label:

  • protein_id
  • Name
  • ID
  • gene
  • label
  • note

If none of these are found, it will display the type with the location.

You need to provide a values for any of these field for any feature you wish to have a label.
Furthermore, labels are only displayed when the box is large enough.

If you always want them to display, there is a configuration option for that. Either available through the menu or in the config file you make for your instances.

track:forceFeatureLabels=true

Short read track

Short read are displayed in the Short read track as color boxes that are in some cases connected with pink lines. The pictures belows should give you an idea what the meaning is of the various visual clues.

Short read track, zooming in from left to rightShort read track, zooming in from left to right

Default color scheme

Color Description
Green Read mapped to the forward strand from a sense fragment in a PE library or from a single end library
Blue Read mapped to the reverse strand from a sense fragment in a PE library or from a single end library
Cyan Read mapped to the reverse strand from an anti-sense fragment in a PE library
Orange Read mapped to the forward strand from a anti-sense fragment in a PE library
Yellow Mismatch between the read and the reference, the read nucleotide will be shown when zoomed in
Red Gap/deletion in the read
Black Insertion in the read. Hover over them to see inserted bases.
Gray Insertion in the read that is a multiple of 3. Hover over them to see inserted bases.
Purple/Pink Connection between two reads from a paired-end library (thin line), or connection between parts of a single read aligned over a splice junction (thick line). Both the PE connections and splice junctions ones will be shown simultaneously in data sets that have that information.

Note that some older alignment software does not include the correct information in the BAM file and that the color scheme may be off for those files. Use common sense when interpreting results!

Overview of visual clues in the short read trackOverview of visual clues in the short read track

Hovering over reads shows detailed information about the readHovering over reads shows detailed information about the read

Pile up track

The pile up track can consists of to information parts. The first one, the coverage plot, is always present, the second, the SNP plot, is only displayed if the loaded data set has the required information.

Typically coverage-only data files are TDF files, while coverage+SNP files are prepared using samtools pileup. More information on preparing pile-ups

Pile up track overviewPile up track overview

Detailed description of component of the pile up track.Detailed description of component of the pile up track.

Multiple alignment track

Multi-fasta/ClustalW multiple alignment

Multi-fasta data can be displayed on three zoom levels.

  1. Zoomed out: Will show conservation plots.
  2. Medium zoom: Shows conservation as a gray scale. Gaps in the alignment are displayed in red.
  3. Zoomed in: Shows the individual nucleotides. Reference gaps are in yellow, alignment gaps in red . At the bottom of the track, the sequence logo for the aligment is shown.

MAF formatted multiple alignment
Details on the MAF format
Demo video showing the multiple alignment track.
Watch video full screen in HD mode for best quality, the video contains no sound

Multiple alignments can be displayed in three zoom levels.

The most detailed level shows mismatches and gaps for each alignment. Hovering over the track displays the names of the species on the left.

On the middle level, we can still hover the track to see the species. An alignment on the forward strand is drawn in green, one to the reverse strand in blue.

When we zoom even further out, the alignments are displayed in gray. The more species align to a certain part of the reference sequence, the longer the gray line. Individual species are not displayed anymore.

After this, zooming further out will not display alignments anymore because of performance reasons.

Color key:

Gray mismatch with reference
Red gap in alignment
Green Alignment to forward strand
Blue Alignment to reverse strand

Wiggle track

No screenshots or description available yet.