Trying To Open 2 Files In A Visualizer In Galaxy To Compare Variants

Question

[corn8bit]

I'm doing a demo for some folks and need to visually point out some variants in a couple bam files. Is there an easy way to do this in Galaxy?

I can do it just fine in IGV by itself by just opening both files and the reference.

Edit: To be clear, I just want to launch IGV (or anything) with multiple files from Galaxy. I don't see this in the docs either.

Answer 1

[Björn]

Each bam, bed, vcf file can be visualized in several genome viewers, if configured. If IGV support is enabled, open your IGV, go back to your Galaxy session, click visualize with IGV (local) and your dataset will be automatically transferred to your local IGV. You can visualize as many as possible files from Galaxy in the same IGV session.

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Bjoern

Answer 2

[Jennifer Hillman Jackson]

You can launch Trackster (the Galaxy native "Visualization" tool) directly from one dataset, then add in any other dataset from any of your histories or from Shared Libraries. Or, you can start the Visualization directly without any datasets, and add datasets in all at once, or in later in increments. This is probably the simplest way to view data.

Other display options appear within expanded dataset as lines like "display in IGB Local Web". You can click on multiple datasets and they should all load into the same session at the remote host.

As noted above, datasets can also just be added to many external vis tools. But the above are the integrated tools.

jen