The Ensembl and UCSC genomes should be identical. You need to
be careful to compare versions of genomes. There are numerous
versions of the genomes at UCSC. Some scaffold based assemblies
have different presentation organizations between UCSC and Ensembl.
There is usually a translation table in the UCSC database. See also:
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \
-e "select * from trackVersion;" hgFixed
Note the entries where dateReference="current"
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \
-e 'select * from trackVersion where dateReference="current";' hgFixed
--Hiram
----- Original Message -----
From: "vaibhav jain" <[email protected]>
To: [email protected]
Sent: Friday, March 25, 2011 6:59:12 AM
Subject: [Genome] Concordance between Ensemble coordinates and UCSC
coordinates
Respected sir/madam,
I have downloaded some alternative splice site data from Ensemble Genome
Browser, data contains coordinates (start, end) for each site and now i want
to match this data with some data which I downloaded from UCSC Genome
Browser.
If the coordinates of both the browser's is different than I wont get the
correct result. So I would like to know whether the coordinates of both the
browser is same or different.
--
Vaibhav Jain
Research Scholar @IGIB
New Delhi, INDIA
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