Re: [galaxy-user] Adding the Hydra genome to Galaxy
Hello Rob, We will add this to our to-do list for new genomes. Thanks for sending the Genbank information! Next time, if you could send requests to galaxy-user, that would be very helpful for the team. Best, Jen Galaxy team On 1/3/11 12:37 PM, Rob Steele wrote:
Hi Jennifer, Would it be possible to get the Hydra genome assembly added to Galaxy? It has been published and is available in GenBank under accession number ABRM00000000.
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
-- Jennifer Jackson http://usegalaxy.org
Hi Jen et al., Sorry to be a pest, but do you have an estimate for when the Hydra genome will be added to Galaxy? Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page On 1/3/11 12:53 PM, Jennifer Jackson wrote:
Hello Rob,
We will add this to our to-do list for new genomes. Thanks for sending the Genbank information!
Next time, if you could send requests to galaxy-user, that would be very helpful for the team.
Best,
Jen Galaxy team
On 1/3/11 12:37 PM, Rob Steele wrote:
Hi Jennifer, Would it be possible to get the Hydra genome assembly added to Galaxy? It has been published and is available in GenBank under accession number ABRM00000000.
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
Hello Rob, This genome is being worked on right now and should be available soon. Please feel free to check back a few weeks again for an update if you do not see it by then. Thanks! Jen Galaxy team On 2/14/11 3:20 PM, Rob Steele wrote:
Hi Jen et al., Sorry to be a pest, but do you have an estimate for when the Hydra genome will be added to Galaxy?
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
On 1/3/11 12:53 PM, Jennifer Jackson wrote:
Hello Rob,
We will add this to our to-do list for new genomes. Thanks for sending the Genbank information!
Next time, if you could send requests to galaxy-user, that would be very helpful for the team.
Best,
Jen Galaxy team
On 1/3/11 12:37 PM, Rob Steele wrote:
Hi Jennifer, Would it be possible to get the Hydra genome assembly added to Galaxy? It has been published and is available in GenBank under accession number ABRM00000000.
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
Hi Jen, How are things progressing with the Hydra genome? Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page On 2/15/11 6:17 AM, Jennifer Jackson wrote:
Hello Rob,
This genome is being worked on right now and should be available soon. Please feel free to check back a few weeks again for an update if you do not see it by then.
Thanks!
Jen Galaxy team
On 2/14/11 3:20 PM, Rob Steele wrote:
Hi Jen et al., Sorry to be a pest, but do you have an estimate for when the Hydra genome will be added to Galaxy?
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
On 1/3/11 12:53 PM, Jennifer Jackson wrote:
Hello Rob,
We will add this to our to-do list for new genomes. Thanks for sending the Genbank information!
Next time, if you could send requests to galaxy-user, that would be very helpful for the team.
Best,
Jen Galaxy team
On 1/3/11 12:37 PM, Rob Steele wrote:
Hi Jennifer, Would it be possible to get the Hydra genome assembly added to Galaxy? It has been published and is available in GenBank under accession number ABRM00000000.
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
Hi Rob, The project ABRM00000000 links to several thousand individual WGS submissions. Are there scaffolds or some type of assembled sequence available? Or, perhaps there an alternate source? Also, did you want us to include the two mitochondrial genomes from NCBI in the main assembly (once we have it?). This is common for us to do, but not required. And finally, if there is a short-hand name for the genome that you and the Hydra community use, we can assign that as the short-label for the genome. Otherwise, we just use the Genus_species_source_date for the label. Some way to distinguish from ACZU00000000 seems important. Thanks Rob, we look forward to your feedback. Jen On 3/6/11 4:21 PM, Rob Steele wrote:
Hi Jen, How are things progressing with the Hydra genome?
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
On 2/15/11 6:17 AM, Jennifer Jackson wrote:
Hello Rob,
This genome is being worked on right now and should be available soon. Please feel free to check back a few weeks again for an update if you do not see it by then.
Thanks!
Jen Galaxy team
On 2/14/11 3:20 PM, Rob Steele wrote:
Hi Jen et al., Sorry to be a pest, but do you have an estimate for when the Hydra genome will be added to Galaxy?
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
On 1/3/11 12:53 PM, Jennifer Jackson wrote:
Hello Rob,
We will add this to our to-do list for new genomes. Thanks for sending the Genbank information!
Next time, if you could send requests to galaxy-user, that would be very helpful for the team.
Best,
Jen Galaxy team
On 1/3/11 12:37 PM, Rob Steele wrote:
Hi Jennifer, Would it be possible to get the Hydra genome assembly added to Galaxy? It has been published and is available in GenBank under accession number ABRM00000000.
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
Hi Jen, The easiest way to refer to this genome would be Hydra_JCVI. This way we know it is the JCVI assembly (ABRM00000000). ACZU00000000 is a separate assembly that was done at Berkeley. Including the two mitochondrial genomes would be a good idea. The many WGS submissions under ABRM00000000 are the scaffolds/contigs from the JCVI assembly. Because we were unable to obtain long-insert clones (e.g. BACs), the assembly is more fragmented than is typical for a metazoan genome assembly, and thus it has more scaffolds/contigs than is typical. Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page On 3/7/11 1:12 PM, Jennifer Jackson wrote:
Hi Rob,
The project ABRM00000000 links to several thousand individual WGS submissions. Are there scaffolds or some type of assembled sequence available? Or, perhaps there an alternate source?
Also, did you want us to include the two mitochondrial genomes from NCBI in the main assembly (once we have it?). This is common for us to do, but not required.
And finally, if there is a short-hand name for the genome that you and the Hydra community use, we can assign that as the short-label for the genome. Otherwise, we just use the Genus_species_source_date for the label. Some way to distinguish from ACZU00000000 seems important.
Thanks Rob, we look forward to your feedback.
Jen
On 3/6/11 4:21 PM, Rob Steele wrote:
Hi Jen, How are things progressing with the Hydra genome?
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
On 2/15/11 6:17 AM, Jennifer Jackson wrote:
Hello Rob,
This genome is being worked on right now and should be available soon. Please feel free to check back a few weeks again for an update if you do not see it by then.
Thanks!
Jen Galaxy team
On 2/14/11 3:20 PM, Rob Steele wrote:
Hi Jen et al., Sorry to be a pest, but do you have an estimate for when the Hydra genome will be added to Galaxy?
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
On 1/3/11 12:53 PM, Jennifer Jackson wrote:
Hello Rob,
We will add this to our to-do list for new genomes. Thanks for sending the Genbank information!
Next time, if you could send requests to galaxy-user, that would be very helpful for the team.
Best,
Jen Galaxy team
On 1/3/11 12:37 PM, Rob Steele wrote:
Hi Jennifer, Would it be possible to get the Hydra genome assembly added to Galaxy? It has been published and is available in GenBank under accession number ABRM00000000.
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
Thanks Rob, This definitely helps - we appreciate the additional info. This is on our high-priority list and Kelly will get back to you if we have more questions. Best, Jen On 3/7/11 1:23 PM, Rob Steele wrote:
Hi Jen, The easiest way to refer to this genome would be Hydra_JCVI. This way we know it is the JCVI assembly (ABRM00000000). ACZU00000000 is a separate assembly that was done at Berkeley. Including the two mitochondrial genomes would be a good idea. The many WGS submissions under ABRM00000000 are the scaffolds/contigs from the JCVI assembly. Because we were unable to obtain long-insert clones (e.g. BACs), the assembly is more fragmented than is typical for a metazoan genome assembly, and thus it has more scaffolds/contigs than is typical.
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
On 3/7/11 1:12 PM, Jennifer Jackson wrote:
Hi Rob,
The project ABRM00000000 links to several thousand individual WGS submissions. Are there scaffolds or some type of assembled sequence available? Or, perhaps there an alternate source?
Also, did you want us to include the two mitochondrial genomes from NCBI in the main assembly (once we have it?). This is common for us to do, but not required.
And finally, if there is a short-hand name for the genome that you and the Hydra community use, we can assign that as the short-label for the genome. Otherwise, we just use the Genus_species_source_date for the label. Some way to distinguish from ACZU00000000 seems important.
Thanks Rob, we look forward to your feedback.
Jen
On 3/6/11 4:21 PM, Rob Steele wrote:
Hi Jen, How are things progressing with the Hydra genome?
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
On 2/15/11 6:17 AM, Jennifer Jackson wrote:
Hello Rob,
This genome is being worked on right now and should be available soon. Please feel free to check back a few weeks again for an update if you do not see it by then.
Thanks!
Jen Galaxy team
On 2/14/11 3:20 PM, Rob Steele wrote:
Hi Jen et al., Sorry to be a pest, but do you have an estimate for when the Hydra genome will be added to Galaxy?
Cheers, Rob
Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700
phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page
On 1/3/11 12:53 PM, Jennifer Jackson wrote:
Hello Rob,
We will add this to our to-do list for new genomes. Thanks for sending the Genbank information!
Next time, if you could send requests to galaxy-user, that would be very helpful for the team.
Best,
Jen Galaxy team
On 1/3/11 12:37 PM, Rob Steele wrote: > Hi Jennifer, > Would it be possible to get the Hydra genome assembly added to > Galaxy? > It has been published and is available in GenBank under accession > number > ABRM00000000. > > Cheers, > Rob > > Rob Steele, Ph.D. > Professor > D240 Medical Sciences I > Department of Biological Chemistry > School of Medicine > University of California, Irvine > Irvine, CA 92697-1700 > > phone: 949-824-7341 > e-mail: resteele@uci.edu > fax: 949-824-2688 > web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page >
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
Hi, Hydra_JCVI is now available in Galaxy for several tools, including NGS analysis. Let us know if you run into any problems using it. Regards, Kelly
Hi Kelly, Thanks much! Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: resteele@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page On 4/6/11 2:02 PM, Kelly Vincent wrote:
Hi,
Hydra_JCVI is now available in Galaxy for several tools, including NGS analysis. Let us know if you run into any problems using it.
Regards, Kelly
participants (3)
-
Jennifer Jackson -
Kelly Vincent -
Rob Steele