Re: Upload of most recent genome data for Apis mellifera onto Galaxy and/or NCSC web sites?

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Re: Upload of most recent genome data for Apis mellifera onto Galaxy and/or NCSC web sites?

Anton Nekrutenko
Diana:

It is best to direct such requests to [hidden email] mailing list, which I am doing. Adding this genome should be possible, but will take us some time. 

Thanks,

anton

Anton Nekrutenko




On Sep 12, 2011, at 1:23 PM, Diana Cox-Foster wrote:

Hi, Anton--- I am currently doing a NGS project and want to compare the sequencing data to the Apis mellifera genome.  Unfortunately, the genomes on Galaxy and the UCSC website are quite outdated.  I am planning to do another sequencing project that would also benefit from having the newest version as well.



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Re: Upload of most recent genome data for Apis mellifera onto Galaxy and/or NCSC web sites?

Jen Hillman-Jackson
Hi Diana,

As Anton mentioned, we can add this genome to our working list. A
check-in with UCSC about their plans for an update seems appropriate and
that will be part of our prioritization of this genome.

Meanwhile, the fastest way for you to start working with this genome
right away is to load it into your history as a custom reference genome.
Simply upload the fasta version via FTP and most tools will function
just as if the genome was native to Galaxy.

You can even create your own custom browser for the genome using the GTB
(Galaxy Track Browser). The GTB is undergoing active development right
now, so you will notice new features over the near-term. Currently,
visualization for custom genomes is based on coordinates only, but
adding in the reference genome back-bone sequence itself is a priority
and will be added in soon. Any data mapped to the reference genome can
be visualized and there is feedback between the browser and your working
histories. Please see:
http://galaxyproject.org/wiki/Learn/Visualization

Thanks for using Galaxy!

Best,

Jen
Galaxy team

On 9/12/11 10:51 AM, Anton Nekrutenko wrote:

> Diana:
>
> It is best to direct such requests to [hidden email]
> <mailto:[hidden email]> mailing list, which I am doing. Adding
> this genome should be possible, but will take us some time.
>
> Thanks,
>
> anton
>
> Anton Nekrutenko
> http://galaxyproject.org
>
>
>
>
> On Sep 12, 2011, at 1:23 PM, Diana Cox-Foster wrote:
>
>> Hi, Anton--- I am currently doing a NGS project and want to compare
>> the sequencing data to the Apis mellifera genome. Unfortunately, the
>> genomes on Galaxy and the UCSC website are quite outdated. I am
>> planning to do another sequencing project that would also benefit from
>> having the newest version as well.
>>
>
>
>
> ___________________________________________________________
> 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/Support
___________________________________________________________
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 Hillman-Jackson
http://galaxyproject.org
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Re: Upload of most recent genome data for Apis mellifera onto Galaxy and/or NCSC web sites?

Diana Cox-Foster
Thanks, I appreciate all your help-- Diana

On Sep 14, 2011, at 9:02 PM, Jennifer Jackson wrote:

> Hi Diana,
>
> As Anton mentioned, we can add this genome to our working list. A check-in with UCSC about their plans for an update seems appropriate and that will be part of our prioritization of this genome.
>
> Meanwhile, the fastest way for you to start working with this genome right away is to load it into your history as a custom reference genome. Simply upload the fasta version via FTP and most tools will function just as if the genome was native to Galaxy.
>
> You can even create your own custom browser for the genome using the GTB (Galaxy Track Browser). The GTB is undergoing active development right now, so you will notice new features over the near-term. Currently, visualization for custom genomes is based on coordinates only, but adding in the reference genome back-bone sequence itself is a priority and will be added in soon. Any data mapped to the reference genome can be visualized and there is feedback between the browser and your working histories. Please see:
> http://galaxyproject.org/wiki/Learn/Visualization
>
> Thanks for using Galaxy!
>
> Best,
>
> Jen
> Galaxy team
>
> On 9/12/11 10:51 AM, Anton Nekrutenko wrote:
>> Diana:
>>
>> It is best to direct such requests to [hidden email]
>> <mailto:[hidden email]> mailing list, which I am doing. Adding
>> this genome should be possible, but will take us some time.
>>
>> Thanks,
>>
>> anton
>>
>> Anton Nekrutenko
>> http://galaxyproject.org
>>
>>
>>
>>
>> On Sep 12, 2011, at 1:23 PM, Diana Cox-Foster wrote:
>>
>>> Hi, Anton--- I am currently doing a NGS project and want to compare
>>> the sequencing data to the Apis mellifera genome. Unfortunately, the
>>> genomes on Galaxy and the UCSC website are quite outdated. I am
>>> planning to do another sequencing project that would also benefit from
>>> having the newest version as well.
>>>
>>
>>
>>
>> ___________________________________________________________
>> 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/Support

**************************************************
Diana Cox-Foster, Professor
Department of Entomology
Penn State University
501 ASI Bldg.
University Park, PA 16802

[hidden email]
Office phone: 814-865-1022
Dept. Office phone: 814-865-1895



___________________________________________________________
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/