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 <j...@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 >> >> ------------------------------**------------------------------** >> ------------ >> >> 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<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<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/
