Question: Fw: Chip-Seq And Gene Ontology With Galaxy-Ucsc
0
Mary Mangan • 40 wrote:
I actually did an exercise that described how to get GO IDs and GO
terms
from UCSC Table Browser at the request of the ENCODE project folks who
are
doing similar stuff.
In the UCSC Table Browser tutorial materials (
http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28 ) click the
Exercises
button. See Exercise 3 to walk through it.
Mary
Mary Mangan, PhD
President
OpenHelix LLC
65 Main St.
Somerville MA 02145
phone: 888-861-5051 x9
email: mmangan@openhelix.com
http://blog.openhelix.com
[mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Oscar V
Camacho
To: galaxy-user@bx.psu.edu
Subject: [galaxy-user] ChIP-Seq and Gene Ontology with Galaxy-UCSC
Hi,
I am currently doing some ChIP-Seq experiments, to analyze the data I
get
from the PeakFinder of my choice I'm using the Galaxy tool from the
UCSC
browser to manipulate my intervals. What I have is a file in .BED
format
with the chromosome number, Start, End of the position and then I
fetch the
closest features and up to this moment everything is perfect but now
that I
have the positions of the nearest features to my putative binding
sites I
would like to get the gene symbol, description y GO for each one of
them in
a sort of table so as I can analyze it later on and make
relationships.
Is there a direct tool between Galaxy and a Gene ontology database?
Any help about this topic will be appreciated.
Thank you in advance.