Hi Vasu,

I'm going to add the function to index BAM files soon, using Picard. In the beginning.... there was no java BAM reader, only SAM, and I added the index then. Indexed BAMs came along later, but that's probably more than you want to know... I think most people will still use Galaxy to index as it can take a long time, but I agree with you on the convenience factor.


Jim


On May 6, 2011, at 9:36 PM, vasu punj wrote:

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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Galaxy analysis and other features on the public server
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using "reply all" in your mail client.  For discussion of
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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