Hi Stephen, The options in the prior post are still current for the Galaxy main server, however a direct method is something the team would like to consider. I have opened a ticket a bitbucket to track progress: http://bitbucket.org/galaxy/galaxy-central/issue/727/add-a-tool-to-do-bam-to... Thanks for bringing up this topic again, it is a great idea, Best, Jen Galaxy team On 2/27/12 3:05 AM, Stephen Taylor wrote:

Hi,

What is the 'official' method of converting a BAM file to a bigwig on the public server?

I saw this post:

http://gmod.827538.n3.nabble.com/SAM-to-bigbed-td3059499.html

but it seems a bit long winded given the commonness of the operation.

On our local galaxy we installed from the Tool Shed:

BAM to BigWig Calculates coverage from a BAM alignment file

Which seems the obvious choice to make available.

Thanks,

Steve ___________________________________________________________ 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:

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/

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support