Visualization in Galaxy Trackster,Circster,IGV

Visualizing data from Galaxy

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".

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

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)

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

Viewing data in a New or Saved Visualization

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

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.

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.

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.

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

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’.

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.

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.

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

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.

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.

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

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.

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

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 .

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

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.

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

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.

Save and Exit

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.

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

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.

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

THANK YOU!