Hi Aaron,
I don't - but I am not sure if it is there anyway (didn't find or missed
it). This will take some research, unless someone else on the list knows
where to look and can send info. My quick scan didn't find it.
I checked "Get Data -> GrameneMart Central server", since I saw some
documentation at one of these sites yesterday (maybe the last link I
sent, with all the rice resources listed) that noted that rice anno data
was now available there. But when I just checked the builds, and it
wasn't this strain. "BioMart Central server" also has the other strain.
I would look around at IRGSP or the other resources in that last link. I
did see that Ensembl (next to last link before) had many files for
download, including one where they mapped annotations (SNPs, I think)
from the IRGSP build to the MSU build, which means they had the starting
IRGSP file to begin with. So even if it is not in the download, they may
have the sources documented somewhere (which would tell you where to
fetch it and potentially gene annotations as well), or you could write
them (or the IRGSP project) directly to find out what they recommend.
You could also search seqanswers.com to see if anyone else was
looking/found the annotation data.
Too bad iGenomes did not pick this up, since if you are using RNA-seq
tools, the extra attributes will maximize what Cuffdiff results you can
produce. It couldn't hurt to ask them to add it to the set, I'm sure
they get requests all the time. I know the MSU build is popular, but
both strains are important, and IRGSP is public without any
restrictions, which has certain advantages of course. Galaxy only
includes the IRGSP build as a native index for this reason. But you
could use the MSU build if you really wanted - and meet the usage
criteria - as a custom reference genome:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
Wish I could just find this for you! But I think this will take a big of
digging and then you'll have to make a call about reliability of the
source, resolve format issues (if any), that sort of thing - so
investigating this on your own is a better path in the absence of a
definitive go-to source. I've tried to share all the leads I could find.
If you do find a good file and it works well, please consider sharing on
the Public server (with the source well documented).
Good luck!
Jen
Galaxy team
On 12/14/12 7:33 AM, Aaron P Smith wrote:
Hi Jen,
Do you have a direct link for the gene coordinates file (GFF?) from
NCBI for the rice genome?
Thanks,
Aaron
______________________________
Aaron Smith, Ph.D.
Assistant Professor
Biological Sciences
Louisiana State University
202 Life Sciences Building
Baton Rouge, LA 70803
[email protected] <mailto:[email protected]>
http://www.smith.biology.lsu.edu/lab
*From:*Jennifer Jackson [mailto:[email protected]]
*Sent:* Thursday, December 13, 2012 11:51 AM
*To:* galaxy-user
*Cc:* Aaron P Smith
*Subject:* rice reference genome
Hello Aaron,
The genome was obtained from Genbank:
http://www.ncbi.nlm.nih.gov/genome/10
http://www.ncbi.nlm.nih.gov/assembly/313038/
Download links can be found at the International Rice Genome
Sequencing Project (IRGSP), but, we source from NCBI directly whenever
possible.
http://rgp.dna.affrc.go.jp/E/IRGSP/index.html
http://rgp.dna.affrc.go.jp/E/IRGSP/Build4/build4.html
These resources may also be helpful in general:
http://www.gramene.org/resources/
http://plants.ensembl.org/Oryza_sativa/Info/Index
http://rice.genomics.org.cn/rice/link/link.jsp
Best,
Jen
Galaxy team
ps. Going forward, please use the mailing list, [email protected]
<mailto:[email protected]>, for new questions to help us out with
tracking. Thanks!
On 12/13/12 9:11 AM, Aaron P Smith wrote:
Hi Jen,
I'm trying to obtain the coordinates for the rice genome used in
Galaxy to compare some sequences from another source. Can you
direct me to the version of the genome used in Galaxy
(oryza_sativa_japonica_nipponbare_IRGSP4.0)?
Thanks!
Aaron
--
Jennifer Jackson
http://galaxyproject.org
--
Jennifer Jackson
http://galaxyproject.org
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