One of the problem is IGV dont have option of creating index file so one has to 
create index file in Galaxy first to  view in IGV. Jim I have been using IGV 2 
beta version it is great work but How hard is to include index functionality 
with in IGV. I know we can use sam tools also but just for convinence if it is 
not that much of work.
Vasu

--- On Fri, 5/6/11, Sean Davis <ssdav...@mail.nih.gov> wrote:


From: Sean Davis <sdav...@mail.nih.gov>
Subject: Re: [galaxy-user] RNA seq analysis
To: "Austin Paul" <austi...@usc.edu>
Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>, 
"puvan...@umn.edu" <puvan...@umn.edu>
Date: Friday, May 6, 2011, 8:02 PM


IGV reads BAM files just fine; no need to convert to SAM.

Sean


On Fri, May 6, 2011 at 8:45 PM, Austin Paul <austi...@usc.edu> wrote:


There are many ways.  I typically use IGV.  It needs a sam file, so I first 
convert the bam to sam in galaxy, then download the sam file.  In IGV, I upload 
the reference and the sam file, then use IGVtools to index the sam file, then I 
can visualize the data.
 
Austin

On Fri, May 6, 2011 at 5:30 PM, <puvan...@umn.edu> wrote:

Hello

I was able to run RNA seq data against a custom build genome. How can I 
visualize the results. I tried via trackster and unfortunately I couldn't. Can 
you help me?


Thanks

Sumathy 



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The Galaxy User list should be used for the discussion of
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