[DAS] Displaying UCSC contig data on Ensembl

[Angie Hinrichs]

The latest UCSC human freeze is NCBI build30, like Ensembl.  Our build 
has 1395 NT's.  There are 1381 NT's referenced in this file:

ftp://ftp.ensembl.org/pub/human-8.30/data/mysql/homo_sapiens_core_8_30a/static_golden_path.txt.table.gz

These are the 14 NTs in UCSC's build that are not in the above file:

NT_033166
NT_033167
NT_033168
NT_033170
NT_033950
NT_033951
NT_034872
NT_034873
NT_034874
NT_034875
NT_034876
NT_034877
NT_034878
NT_034879

That is the set of all unplaced contigs in chromosome 6 in UCSC's 
build (UCSC's "chr6_random" or "6_random" in our DAS server)

Ensembl folks, any reason those NTs were omitted?  (since other 
chromosomes' unplaced contigs were included, for example NT_034507 
which is unplaced on chr2)

Angie

angie@soe.ucsc.edu
Software Developer, UCSC CBSE / Genome Bioinformatics Group

On Fri, 4 Oct 2002, Zayed Albertyn wrote:

> Hi all
> 
> I recently tried out the DAS feature on ensembl with little success
> because it does not convert NT contig clone coordinates. I am using the
> latest UCSC freeze and the static goldenPath table in Ensembl_core_human
> database doesnt seem to list all these NT clones.
> 
> Has anybody been successful at using this feature with goldenPath
> coordinates? If so I would appreciate some input.
> 
> Z
> 
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