The Chromosome view can be invoked from some data nodes on the Analysis tab, giving a global overview of the results; or from certain Task report or result pages, providing a focused view, i.e. pointing to a specific feature of interest.
Running a Chromosome View Task from a Data Node
On the Analysis tab, selecting a data node containing aligned reads, variants, gene or transcript counts, or feature lists, shows Chromosome view in the Visualization section of the context-sensitive menu (Figure 1).
If Partek Flow has no information on the genome build, you will need to provide the species and genome build in a subsequent dialog (not shown). Otherwise, chromosome view will come up directly.
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 menu). When invoked in the aforementioned way, the default visualization in the Chromosome view is the first 100,000 bases of the first chromosome.
Browsing directly to a location directly from a Task Report
Another way to get the Chromosome view is through a Task report. You can launch the viewer by selecting the chromosome icon in the View column (Figure 3) of GSA or View Variants report.
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).
Additional Assistance
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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