Hi Alessia,

Shamsher is correct, Trackster is a great choice for viewing data.

The Galaxy Track Browser (aka Trackster) has several new features and more coming up in the next few weeks at the Main instance. This tutorial covers a basic RNA-seq analysis that includes visualization:
http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

And this wiki explains the details. One brand new feature (undocumented) allows a custom genome to be used in fasta format from your history (same basic instructions as in the wiki for a custom genome browser creation, but use the fasta file instead of a .len file). So whether your genome is native to Galaxy, or UCSC, or not, Trackster can display multiple tracks at full chromosome or zoomed view with user-defined display options:
http://wiki.g2.bx.psu.edu/Learn/Visualization

Hopefully this will work out for you!

Best,

Jen
Galaxy team

On 11/9/11 9:37 AM, Alessia D wrote:
How do people on this mailing list usually visualize Tophat and/or
Cufflinks results (eg. tracks on UCSC browser)?

I have only this once before, and I started with a .wig file that I
uploaded to the genome browser, however it looks like Tophat does not
give any .wig file in the output.  Suggestions?

Thanks!

A





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