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: reste...@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: reste...@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: reste...@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: reste...@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
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