Track height in trackster

[Richard_Naiberg]

When a load a number of tracks, I can only see a sliver of the output.

Here is one view

here is another of the same output

How can I see them all at the same time?

[jennaj]

Hello @Richard_Naiberg

Trackster is a bit of a legacy tool. IGV is usually a better choice.

That said, try this:

1. For the first track, create a new Trackster session. Give it a unique name. Save it.
2. Add more tracks into that same Trackster session.
3. Use the icons above the track to change the shape. Use the “pack” and “full” options to see more details. (somewhat similar to UCSC’s browser).
4. The icons are are cut in half in your screenshot – and are next to the track name on the right of the screen, to the left of the dataset name, above the data.
5. This will require that your datasets all have an assigned “database” metadata key, same as for IGV. Otherwise, these tools don’t know how to “map” the data onto the common genomic backbone.
6. If you have a custom genome, you can create a custom database key for it, and Trackster can use it.
7. IGV can use a custom genome, too, but it will require setting up the custom genome in Galaxy and IGV (different application needs instructions).

This forum has instructions for the custom genome build parts, including for adding a custom genome to IGV. Let me know if you cannot find something and I’ll search and link those back here.

[jennaj]

Update: Please try using IGV or UCSC instead. Mark Trackster as deprecated in the UI · Issue #658 · galaxyproject/usegalaxy-tools · GitHub

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Ah… I remember!! The buttons do not stay active when hovering over them. Forgot.

This will not be fixed. Try using IGV instead. Trackster is legacy – we keep it around because we try not to remove anything, but it should probably be at least marked as deprecated.

We don’t post movies here … but the buttons flicker between these two states, when the cursor moves over the buttons they flicker away.

I think this was only for some datatypes, not all, but cannot remember which. Definitely a problem for BAMs, as in the example above.

Sorry for the confusion and hope that helps!

I decided to make a ticket for the problem, please see if interested → Mark Trackster as deprecated in the UI · Issue #658 · galaxyproject/usegalaxy-tools · GitHub