Thanks Jim,
 
Vasu
 
--- On Fri, 5/6/11, Jim Robinson <jrobi...@broadinstitute.org> wrote:


From: Jim Robinson <jrobi...@broadinstitute.org>
Subject: Re: [galaxy-user] RNA seq analysis
To: "vasu punj" <pu...@yahoo.com>
Cc: "Austin Paul" <austi...@usc.edu>, "Sean Davis" <sdav...@mail.nih.gov>, 
"galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>, 
"puvan...@umn.edu" <puvan...@umn.edu>
Date: Friday, May 6, 2011, 9:01 PM


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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