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 <ssdavis2@mail.nih.gov> wrote:

From: Sean Davis <sdavis2@mail.nih.gov>
Subject: Re: [galaxy-user] RNA seq analysis
To: "Austin Paul" <austinpa@usc.edu>
Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>, "puvan001@umn.edu" <puvan001@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 <austinpa@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, <puvan001@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
Galaxy analysis and other features on the public server
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