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 _______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:   http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at:   http://lists.bx.psu.edu/