Visualization in Galaxy Trackster Circster IGV 0 Visualizing

Visualization in Galaxy Trackster, Circster, IGV 0

Visualizing data from Galaxy 1

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. 2

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, big. Wig, big. Bed, bed. Graph, and VCF datasets from within Galaxy. • Works with large NGS/HTS datasets. 3

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->visualization. Tutorial-RNA-Seq gff 3 vcf Bed. Graph Bed Bam wig Bigwig gtf Overflow beyond listed maximum/minimum value indicated by red region (Histogram) or red dot (Line) 4

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. History Panel in Galaxy 5

Viewing data in a New or Saved Visualization 6

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

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. 8

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. 9

Display modes in Trackster Visualization by two track classes: - Line Tracks: display quantitative data along a y-axis - wig, big. Wig, big. Bed, Bed. Graph -Drawing modes: Histogram, Line, Filled, Intensity 10

Display modes in Trackster(2) Feature. Tracks: display feature interval data - BED, BAM/SAM, gff, gtf, vcf - Drawing modes: Automatic, Coverage, Dense, Squish, Pack Display modes for a gff 3 track shown here. 11

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’. 12

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. 13

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. 14

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 15

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. 16

Circster visualization Example Circster visualization with mapped RNA-seq reads and interaction data. Goecks et al. A Zoomed–in image of the visualization. Panning and zooming around the view results in more detailed data for visible regions. 17

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

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. 19

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

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 3, Bam, big. Wig, big. Bed, vcf formats. 21

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 22

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. 23

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 24

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. 25

Save and Exit 26

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. 27

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

Comparison between Trackster and IGV Feature Trackster (Circster) IGV Visualize datasets from Galaxy without downloading. Yes Visualize multiple datasets using circular layout Yes No Running location Server Local Work sessions can be saved Yes* 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. Yes 29

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

THANK YOU! 31