0. Visualization in Galaxy
Trackster,Circster,IGV

1. Visualizing data from Galaxy

2. Visualization options in Galaxy
Several datasets in Galaxy can be visualized directly on UCSC, IGB, IGV, Ensembl. You can also click on the fourth icon below the dataset name to ‘Visualize’ your dataset in Trackster, Circster or Scatterplot.
why is this good to have visualization in galaxy? Because it allows you to check your data directly and easily right after mapping (bam files visu) or at each step of processing ie "do I have signal in my positive controls".

3. What is Trackster?
Galaxy's visualization and visual analysis environment.
Genome browser for high throughput sequencing data.
It lets you visualize your SAM/BAM, BED, GFF/GTF, WIG, bigWig, bigBed, bedGraph, and VCF datasets from within Galaxy.
Works with large NGS/HTS datasets.
More details can be found on the Galaxy Wiki Tutorial

4. Visualizing various formats in Trackster
Shown here are datasets of different formats visualized in Trackster. All of them are available in the data library: Training->visualizationTutorial-RNA-Seq
gff3
vcf
BedGraph
Bed
Bam
Gff3- coverage
Vcf- coverage
Bedgraph-Histogram
Bed-Auto/Squish
Bam- Auto/Squish
Wig/Bigwig- Histogram
Gtf- auto/squish
wig
Bigwig
gtf
Overflow beyond listed maximum/minimum value indicated by red region (Histogram) or red dot (Line)

5. Visualizing data from your Galaxy History in Trackster
Datasets in Galaxy can be easily visualized in Trackster by clicking on the ‘Visualize’ icon under the dataset name.
Shown here is the ‘mapped4.vcf’ dataset from
Shared Data->Data Libraries->Training->visualizationTutorial-RNA-Seq.
History Panel in Galaxy

6. Viewing data in a New or Saved Visualization

7. Viewing data in a New Visualization
A ‘Browser name’ should be entered and the Reference genome build selected.

8. Navigating in Trackster
Selecting a chromosome
Typing in the desired location
The Floppy Disc icon in the upper right corner is used to save the visualization.

9. Adding Tracks to the saved visualization
The first icon in the upper-right corner of the Trackster window is used to ‘Add Tracks’.
Datasets can be added from any of your Histories or Data Libraries.

10. Display modes in Trackster
Visualization by two track classes:
- Line Tracks: display quantitative data along a y-axis
- wig, bigWig, bigBed,BedGraph
-Drawing modes: Histogram, Line, Filled, Intensity
Intensity: show the data point as a gradient of the current y-axis range (darker is more).
Filled: fill region from the bottom of the track to the data point.
Line: connect the data points with a line. Red dot indicates overflow beyond the listed maximum/minimum value.
Histogram: fill region between x-axis and the data point. Red region indicates overflow beyond the listed maximum/minimum value.

11. Display modes in Trackster(2)
FeatureTracks: display feature interval data
- BED,BAM/SAM, gff, gtf, vcf
- Drawing modes: Automatic, Coverage, Dense, Squish, Pack
Display modes for a gff3 track shown here.
-Squish- draw exons but not strand/labels
-Pack- draw exons, strand, and labels
Dense- Everything stacked on top of one another
Coverage/Histogram- Show no. of features in binned regions

12. Changing track settings
Max/min values set automatically if not specified by user via ‘Edit settings’.
Colour change of tracks also possible via ‘Edit settings’.

13. Other Features in Trackster
Zooming in and out on tracks
Dynamic filters based on feature attribute values.
Tool parameter settings and Tool Parameter space visualization for Cufflinks datasets.
Composite tracks.

14. Visualizing in Circster
Clicking on the fourth (circular) icon in the upper-right corner of the Trackster window will visualize the same datasets in Circster.
Adding tracks from the ‘Additional’ folder in the training data library will result in the visualization shown below. The interactions given by the ‘chrint’ format make up the arcs in the centre.

15. What is Circster?
Circos-style viewer for rendering genome-wide data on the Web.
Circos - software package for visualizing data and information in a circular layout.
Non-genomic data visualized by Circos

16. How is data visualized with Circster?
Position-based data (e.g., binding affinity, gene expression) laid out in concentric circles representing chromosome position.
Chromosome interaction data (e.g., three-dimensional interactions, gene fusions) denoted as arcs on the inside of the position data.
Datasets can be added easily.
Ideal for exploring relationships between objects or positions.
Better visualization for whole genome data.

17. Circster visualization
Example Circster visualization
with mapped RNA-seq reads and interaction data.
A Zoomed–in image of the visualization.
Initially, Circster shows the complete genome, and all data is visible for all datasets. Circster uses the D3 framework to render genomic data as SVG. Using SVG paths to display complex objects such as histograms (e.g. coverage data) and line data (e.g. conservation data) limits the number of objects created and makes the visualization scalable to a large number of datasets.
Figure 3 shows a Circster visualization for mapped RNA-seq reads from both cancer cell lines and normal tissue, as well as potential chimeric transcripts from ChimerDB 2.0 [18].
Panning and zooming around the view results in more detailed data for visible regions.
Goecks et al.

18. Saving and exiting
Save the visualization by clicking on the floppy icon at the upper-right corner.
Go back to the Galaxy main window by clicking on ‘Analyze Data’ in the Galaxy menu.
Analyze Data
Save

19. Caution with Circster
Though Circster is a good way to visualize data in a circular format, we have noted some difficulties while using it.
Changing track settings, deleting tracks not possible directly in Circster.
Unexpected visualization glitches seen.
We would advise you to be cautious with you data while using Circster.

20. What is IGV? Elaborated as ‘Integrative Genomics Viewer’.
Integrated visualization tool for multiple data types and genome annotations.
Data from NGS analysis visualized .

21. Why use IGV? Handles large datasets
Interactive and speedy visualization. Run locally on desktop
View multiple datasets in separate panels on the same pane.
Several track management options (filtering, grouping, sorting) and in-built tools (index, sort, motif finder…)
Direct visualization from Galaxy : bed, wig, gff, gff3, Bam, bigWig, bigBed, vcf formats .

22. Visualizing Galaxy datasets in IGV
2 modes to open Galaxy datasets in IGV:
Web current : Download IGV on your system and open dataset in new window.
Local : To visualize in the already running IGV

23. Visualizing Galaxy datasets in IGV(2)
1.Select the ‘web current’ option for IGV 2.Open the downloaded jnlp file with ‘Java Web Start’ 3. You will be asked for authentication. Please enter your embl username and password.

24. Visualizing Galaxy datasets in IGV(3)
This is what you should be able to visualize at first.
Select a particular chr or type in the desired location

25. Whole genome view in IGV
The whole genome can be visualized by selecting the ‘All’ option from the Chromosome drop-down menu in the Tool Bar.
When you load genomic data, IGV displays the data in horizontal rows called tracks. Typically, each track represents one sample or experiment. For each track, IGV displays the track identifier, one or more attributes, and the data.
Attribute names are listed at the top of the attribute panel. Colored blocks represent attribute values, where each unique value is assigned a unique color. Hover over a colored block to see the attribute value. Click an attribute name to sort tracks based on that attribute value.

26. Save and Exit

27. Session File
A session file (XML) contains information about the genome, locus, data files opened in IGV when the session was saved.
It also contains detailed information about the tracks which were saved.
Sessions can be easily restored in IGV at a later point.

28. Other IGV features Changing track settings
igvtools- index, sort, count
Sorting, filtering, grouping tracks
Motif finder
Specific search

29. Comparison between Trackster and IGV
Feature
Trackster (Circster)
IGV
Visualize datasets from Galaxy without downloading.
Yes
Visualize multiple datasets using circular layout No
Running location
Server
Local
Work sessions can be saved
Yes*
Visualize data from Galaxy without installing any software beforehand.
Yes/No
In-built tools to create index, manage tracks (sort,group,filter) and find motifs.
Limited.
Running location- Trackster runs on the server and uses the server resources.IGV – rins on your system. No sharing of resources.
Work sessions- In Trackster, sometimes the order of tracks is not preserved. But, IGV sessions are stored as XML files on your system and all the settings are preserved.
In-built tools: Trackster- Only changing track colours and setting histogram values possible. Also filtering.

30. Join us for a Galaxy Visualization Training Thu, 17 October – 13h (max 2 hours) Venue: V 207 Register by

31. THANK YOU!