Hi Danny, On 10/28/11 8:53 AM, Muehlschlegel, Jochen D.,M.D. wrote:

Hi Jen,

Great. I am uploading data right now and will try it. It would be a great addition if it worked and I will give you feedback.

On another note, is Galaxy in the meantime able to do a cufflinks, specifically Cuffdiff analysis, on paired-end data ?

Yes, this options is included on the CuffDiff tool form as an option. Paired vs mate paired data questions would be best directed to the tool authors at tophat.cufflinks@gmail.com. Best, Jen Galaxy team

Thanks

Danny

On 10/27/11 4:56 PM, "Jennifer Jackson"<jen@bx.psu.edu> wrote:

...

Hi Danny,

A beta GATK pipeline is available on our Test instance at: http://test.g2.bx.psu.edu/

Feedback about the tool suite is welcomed!

Best,

Jen Galaxy team

On 10/27/11 1:08 PM, Muehlschlegel, Jochen D.,M.D. wrote:

...

Hi,

Do you host GATK on the Galaxy server? If not, is there a way to call SNPs from NGS (RNA-seq) data using Galaxy ?

Thanks

Danny

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