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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___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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http://lists.bx.psu.edu/ ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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