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 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%20Tu... 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_applica... https://bitbucket.org/galaxy/galaxy-central/src/c510097f7018/universe_wsgi.i... (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
------------------------------------------------------------------------
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
___________________________________________________________ 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: