Question: Rice Reference Genome
0
Jennifer Hillman Jackson ♦ 25k wrote:
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
--
Jennifer Jackson
http://galaxyproject.org