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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