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The Chromosome view
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in Partek Flow is a visualization tool for next-generation sequencing (NGS) and microarray data. The viewer can display different types of information, including aligned reads, genomic databases (e.g. genes, transcripts, or variants), isoform proportions, and reference sequence.
This chapter will illustrate how to:
- Launch the Chromosome view
- Navigate through the view
- Select data tracks for visualization
- Visualize the results using data tracks
- Annotate the results
- Customize the view
Launching the Chromosome View
Figure 1: Accessing Chromosome view via the toolbox (the content of the Visualisation section depends on the selected data node)
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A new Chromosome view task node will be added to the canvas (Figure 2) and in order to invoke the viewer <double-click> on the node (you can also select it and then go to Task report in the toolbox). When invoked in the aforementioned way, the default visualization in the Chromosome view is the first 100,000 bases of the first chromosome.
Figure 2: Selecting Chromosome view from the toolbox adds a Chromosome view task node to the canvas. To open the view, <double click> on it
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Figure 3: Accessing the Chromosome view from results table (mouse-over balloon is visible when hovering over the chromosome icon). The image is an example, based on gene expression pipeline
In that case, the Chromosome view will browse directly to the selected genomic location (i.e. a transcript or a variant, depending on the pipeline).
Navigating Through the View
A user can browse through the results by using one of the tools in the navigation bar (on the top of the view; Figure 4). Select tracks tool is the topic of a separate section, while the remaining tools are described below.
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Start
Zoom-in
Figure 8: Using <left-click> & dragging mouse to zoom into a region of genome (start magnification shown on the left). After releasing the left mouse button, Partek Flow will zoom into the highlighted region (right panel; an example is shown)
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When panning mode is activated, the appearance of the cursor will change to four arrows (Figure 9). <Left-click> and drag the canvas to the left or to the right to move upstream or downstream in the genome, respectively.
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Selecting Data Tracks for Visualization
Partek Flow plots genomic information on the canvas and is organized into horizontal sections called tracks. The exact number, type, and presentation of tracks depend on several factors, such as the underlying pipeline, available annotation, and the level of zoom. The tracks are added, removed, or customized via the Select tracks dialog (Figure 13).
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Visualizing the Results Using Data Tracks
Data tracks section of the Select tracks dialog enables you to specify the tracks for visualization on the canvas. An overview of the available track types is provided in Figure 16. Note that not all tracks are visible at all times and that their presence depends on the zoom level. The tracks can be customised and their appearance changed by using the control panel on the right.
Alignments track
Isoform proportion track
Variants track
Amino acids track
Reads pileup track
Probe intensities track
Will change because of KB-5969
Figure 16: Data tracks in Chromosome view (examples)
Alignments Track
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Isoform Proportion Track
The Isoform proportion track displays the reads mapped to transcripts and helps to visualize differential expression and alternative splicing, using standard symbols for exons (boxes) and introns (lines connecting the boxes). The size of each transcript is proportional to the number of reads that map to that transcript. The color indicates the samples to which the reads belong. Figure 18 shows a gene with two transcripts in RefSeq database; the top transcript is more abundant than the bottom transcript and is preferentially expressed in the "blue" condition (labeled as 0 uM). The bottom transcript, on the other hand, seems to be expressed at the same level across all three conditions (i.e. 0 uM, 5 uM, 10 uM). The number and structure of transcripts on the plot depend on the transcript model that was used for mapping.
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Variants Track
Variant tracks show single nucleotide variants (SNVs) and indels, and appear in the Select track dialog if Detect variants task has been performed. Presentation of variants depends on the level of zoom. With low power magnification, SNVs are seen as purple columns and indels are bars (insertions: green bars; deletions: red bars) (Figure 19).
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Amino Acids
Amino acids track becomes available in the Select tracks dialog after completing the Annotate variants task. The actual appearance of the track depends on the zoom level. With low-power magnification, you will see a message View not available at this zoom level, Please zoom in to view amino acids.
When you zoom closer to the genome, all the amino acids become visible as colored boxes (Figure 22) and labeled using the single-letter amino acid code. Alternative amino acids are depicted as additional boxe on the top of the consensus sequence.
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An empty gray box on the top of consensus sequence is used to indicate a STOP codon, which is a consequence of a mutation (Figure 24).
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Reads Pileup Track
Reads pileup track plots the short sequencing reads, as present in the .bam file. The track is not on by default (go to Select tracks to turn it on) and its appearance depends on the magnification; if you are zoomed out a message - Zoom in to view individual reads - will be displayed.
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Probe Intensities Track
Microarray probes are visualised by the Probe intensities track. The probes are shown as bars and their colour depends on the probe intensity, ranging from white (low) to admiral blue (high) (Figure 29).
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Annotating the Results
Cytoband Track
By default, the Chromosome view shows a cytoband track at the top of the canvas. If a cytoband file for your genome has not been added to Partek Flow, a warning will appear (Figure 30). In that case, go to the Library File Management page and download or create a cytoband file.
Figure 30: Warning message indicating that Chromosome view can not be launched because of missing cytoband file
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Figure 31: Cytoband track: highlighted part is currently depicted on the canvas (an example is shown)
Reference Genome
The sequence of the reference genome is added to the Chromosome view by default, as long as it has been added to the respective genome on the Library File Management page. However, its presence (or absence) in the viewer depends on the current magnification. At low power, the track is hidden and you will see the message - Track hidden (zoom to view). At high power, on the other hand, the Reference genome track becomes visible (Figure 32) and is supplemented by the genomic coordinates (below the sequence). A vertical guide helps you to align the bases between Aligned reads and Reference genome tracks. Depending on the reference genome file, some bases may be shown in lowercase letters, symbolizing repetitive sequences, or other sequences masked by a tool such as RepeatMasker.
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The variants will be shown adjacent to the Reference genome track (Figure 33). If the database contains no frequency information on alternative alleles, the alleles will be drawn as bars (an example is the SNP on the left in Figure 33). If the frequency information is available, the relative frequency of each variant will be represented by a column (the SNP on the right in Figure 33).
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Other Annotation Tracks
Additional annotation tracks can be added to the viewer with the help of the Select tracks dialog (Figure 14) as long as they have been associated with the genome you are working on in the Library File Management.
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Figure 36: Transcript database track: a gene with two transcripts is shown as an example. Exons are plotted as boxes and introns as lines connecting them. Untranslated regions (UTRs) are seen as narrow boxes. The arrows indicate directionality
Customizing the View
Controls
Chromosome view can be customized by using the control panel on the left (Figure 37). The Attribute and Order By controls show options depending on the current project, while the content of the Annotate amino acids control depends on the annotation files associated with the current genome build in the Library File Management. In order for any change to take place, push the Apply button.
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Linked
Figure 43: Read histogram Y axis scales. When set to Linked, all the tracks have the same Y axis maximum, which depends on the sample with the highest coverage. Using Independent sets Y axis maximum independently for each sample.
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Reads pileup color: Base
Figure 48: Reads pileup color: colouring of the short sequencing reads by Strand or by Base
Probe color control customizes the appearance of Probe intensities track (Figure 49). When set to Intensity, colour of a probe reflects its intensity, using a colour gradient from white (low) to admiral (high). Alternatively, when Strand is turned on, probes on the reverse strand are in parakeet green, while probe on the forward strand are in sky blue.
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A track can be hidden (meaning it will not be visible) by selecting the red minus, or unhidden by selecting the green plus icon.
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Additional Assistance
If you need additional assistance, please visit partek.com/PartekSupport to submit a help ticket or find regional phone numbers to call Partek support.
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