Add Tribolium genome

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Add Tribolium genome

Brenda Oppert
I thought that the genome sequence for Tribolium castaneum (Tcas3.0) was in the genome pull-down, but I don't see it.  Can it be added?

Thanks,

Brenda
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Re: Add Tribolium genome

Jen Hillman-Jackson
Hello Brenda,

Are you working at http://usegalaxy.org? I just checked and it is still there. Please give this another look.

Thanks!

Jen
Galaxy team


On "Get Data -> Upload File" tool:


Under "Edit Attributes" (found by clicking on a dataset's pencil icon):


On 4/10/14 11:06 AM, Brenda Oppert wrote:
I thought that the genome sequence for Tribolium castaneum (Tcas3.0) was in the genome pull-down, but I don't see it.  Can it be added?

Thanks,

Brenda
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

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

___________________________________________________________
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:

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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Add Tribolium genome

Jen Hillman-Jackson
Hi Brenda,

The examples below are labeled by the tool/user interface location where the two menus are located. Which tool are you using under "Get Data"? Perhaps "UCSC Main"?

Any tool other than "Upload File" accesses an external data source and the available data can vary. It is important to know that the data content included on externally hosted sites is managed by that sites owners. If you are using "Get Data -> UCSC Main", then you are correct in that they do not provide data for this genome, just the ones you list.

When you do locate data for this species that you wish you use (try searching for "Tribolium castaneum" with the tool " EBI SRA ENA SRA"), and import it, the Galaxy locally cached reference genome for Tcas_3.0 is available with several, but not all, mapping tools. It is likely to be added to Bowtie2/Tophat2 sometime in the future.

Thanks!

Jen
Galaxy team

On 4/10/14 2:27 PM, Brenda Oppert wrote:

Hi Jen,


When I go to "get data" and I put "insect" the only pull downs are some Drosophila and Anopheles spp. Is it somewhere else?


Thanks,


Brenda


From: Jennifer Jackson [hidden email]
Sent: Thursday, April 10, 2014 4:18 PM
To: Brenda Oppert; [hidden email]
Subject: Re: [galaxy-user] Add Tribolium genome
 
Hello Brenda,

Are you working at http://usegalaxy.org? I just checked and it is still there. Please give this another look.

Thanks!

Jen
Galaxy team


On "Get Data -> Upload File" tool:


Under "Edit Attributes" (found by clicking on a dataset's pencil icon):


On 4/10/14 11:06 AM, Brenda Oppert wrote:
I thought that the genome sequence for Tribolium castaneum (Tcas3.0) was in the genome pull-down, but I don't see it.  Can it be added?

Thanks,

Brenda
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

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

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

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: Add Tribolium genome

Brenda Oppert
Thanks-found it!  We have a lot of data, but are trying to convert some data to BED format, and I think that this will help.

Brenda
On Apr 10, 2014, at 7:50 PM, Jennifer Jackson wrote:

Hi Brenda,

The examples below are labeled by the tool/user interface location where the two menus are located. Which tool are you using under "Get Data"? Perhaps "UCSC Main"?

Any tool other than "Upload File" accesses an external data source and the available data can vary. It is important to know that the data content included on externally hosted sites is managed by that sites owners. If you are using "Get Data -> UCSC Main", then you are correct in that they do not provide data for this genome, just the ones you list.

When you do locate data for this species that you wish you use (try searching for "Tribolium castaneum" with the tool " EBI SRA ENA SRA"), and import it, the Galaxy locally cached reference genome for Tcas_3.0 is available with several, but not all, mapping tools. It is likely to be added to Bowtie2/Tophat2 sometime in the future.

Thanks!

Jen
Galaxy team

On 4/10/14 2:27 PM, Brenda Oppert wrote:

Hi Jen,


When I go to "get data" and I put "insect" the only pull downs are some Drosophila and Anopheles spp. Is it somewhere else?


Thanks,


Brenda


From: Jennifer Jackson [hidden email]
Sent: Thursday, April 10, 2014 4:18 PM
To: Brenda Oppert; [hidden email]
Subject: Re: [galaxy-user] Add Tribolium genome
 
Hello Brenda,

Are you working at http://usegalaxy.org? I just checked and it is still there. Please give this another look.

Thanks!

Jen
Galaxy team


On "Get Data -> Upload File" tool:
<Mail Attachment.png>

Under "Edit Attributes" (found by clicking on a dataset's pencil icon):
<Mail Attachment.png>

On 4/10/14 11:06 AM, Brenda Oppert wrote:
I thought that the genome sequence for Tribolium castaneum (Tcas3.0) was in the genome pull-down, but I don't see it.  Can it be added?

Thanks,

Brenda
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

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

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


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
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