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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