Re: [galaxy-user] Upload of most recent genome data for Apis mellifera onto Galaxy and/or NCSC web sites?
Diana:
It is best to direct such requests to galaxy-user@bx.psu.edu 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 Unfortunately, the genomes on Galaxy and the UCSC website are quite outdated.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.
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 galaxy-user@bx.psu.edu mailto:galaxy-user@bx.psu.edu 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 Unfortunately, the genomes on Galaxy and the UCSC website are quite outdated.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:
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 galaxy-user@bx.psu.edu mailto:galaxy-user@bx.psu.edu 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:
-- 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
dxc12@psu.edu Office phone: 814-865-1022 Dept. Office phone: 814-865-1895
galaxy-user@lists.galaxyproject.org
-
Anton Nekrutenko -
Diana Cox-Foster -
Jennifer Jackson