GATK

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GATK

Muehlschlegel, Jochen D.,M.D.
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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Re: GATK

Jen Hillman-Jackson
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
>
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>
>
> ___________________________________________________________
> 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

Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: GATK

Jen Hillman-Jackson
In reply to this post by Muehlschlegel, Jochen D.,M.D.
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 [hidden email].

Best,

Jen
Galaxy team


> Thanks
>
> Danny
>
>
>
>
>
>
> On 10/27/11 4:56 PM, "Jennifer Jackson"<[hidden email]>  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
>>>
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>> ___________________________________________________________
>>> 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
>
>

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

Jennifer Hillman-Jackson
http://galaxyproject.org