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 <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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