Re: [galaxy-user] TopHat/Cufflinks visualization
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 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] TopHat/Cufflinks visualization
Ues IGV or Galaxy tracker. On Wed, Nov 9, 2011 at 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 > > > > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] TopHat/Cufflinks visualization
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 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
