Just to add, Trackster is pretty awesome for RNA-seq data and well worth learning to use. If you also want to see it in IGV you can load the BAM and "gtf" files, but you will have to download "gtf" files to your local drive, then load them from the file menu. You can view the Bam without downloading by following Jennifer's instructions below. On Thu, Mar 29, 2012 at 2:59 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

Hello Jianpeng,

Please see step #2 in the RNA-seq tutorial for visualization help: https://main.g2.bx.psu.edu/u/**jeremy/p/galaxy-rna-seq-**analysis-exercise<https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise>

For IGV and other external applications, these links will appear inside dataset boxes that have database/datatype identifiers that meet the criteria for the visualization tool (each is different). Instructions for those that require set-up are in these wikis:

http://wiki.g2.bx.psu.edu/**Admin/Tools/External%** 20Display%20Applications%**20Tutorial<http://wiki.g2.bx.psu.edu/Admin/Tools/External%20Display%20Applications%20Tutorial>

http://wiki.g2.bx.psu.edu/**Admin/Config/Apache%20Proxy<http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy>

When doing the set up, these will be the areas of the source involved for external application:

https://bitbucket.org/galaxy/**galaxy-central/src/**c510097f7018/display_* *applications<https://bitbucket.org/galaxy/galaxy-central/src/c510097f7018/display_applications>

https://bitbucket.org/galaxy/**galaxy-central/src/** c510097f7018/universe_wsgi.**ini.sample<https://bitbucket.org/galaxy/galaxy-central/src/c510097f7018/universe_wsgi.ini.sample>(modify "# -- Display site" as needed)

Loading the data from the RNA-seq tutorial into a history on the main Galaxy server will give you an example of what the links looks like once set up (if you choose to do them all).

Thanks,

Jen Galaxy team

On 3/29/12 6:35 AM, Xu, Jianpeng wrote:

...

Hi ,

I have installed our local galaxy and tried to run some programs. I have run the Tophat with RNA-seq data. There are two output files: accepted_hits, and splice_junctions. Can you tell me how to view the results files? Is there a tool on galaxy that can be used to view the result ? Can I use IGV to view it ?

Thanks a lot.

Jianpeng

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