I have used IGV with the Bam file and one ha sto generate index file which can be done in IGV, it work well. Gbrowser should also be OK. I think new version of IGV provide lot more features than previous one
Vasu.


--- On Fri, 2/18/11, Peter <biopython@maubp.freeserve.co.uk> wrote:

From: Peter <biopython@maubp.freeserve.co.uk>
Subject: Re: [galaxy-user] SAM to GFF ?
To: "Felix Hammer" <hammerf@cip.ifi.lmu.de>
Cc: galaxy-user@lists.bx.psu.edu
Date: Friday, February 18, 2011, 8:09 AM

On Fri, Feb 18, 2011 at 12:35 PM, Felix Hammer <hammerf@cip.ifi.lmu.de> wrote:
>
> Hi Peter,
> thx for the reply.
> You're right I want to display mapped RNA seq data in gBrowse.
> Currently I have the data in SAM format.
> Maybe I can figure out a trick using the text manipulation tools.
> thx,
> Felix

You forgot to CC the mailing list. If you want to use the data in
GBrowse then why not use SAM/BAM directly? I've not tried
it yet but I understand GBrowse can display BAM files... best
asking on their mailing list if you need more details. This
doesn't involve Galaxy directly though...

Peter
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