[Genome] C. elegans assembly ce3

[Hiram Clawson]

Good Afternoon Nathan:

The UCSC ce3 assembly is worm base WS140
The ce4 assembly is worm base WS170
The ce2 assembly is worm base WS120

We never released ce3 from our test server at UCSC.  If you want to work
with that, you can fetch data tracks from ce3 from the test server.
You can get the gene tracks you mention via the "Tables" browser there.

Or, the original GTF files can be fetched from wormbase.
ftp://ftp.sanger.ac.uk/pub/wormbase/FROZEN_RELEASES/WS120
ftp://ftp.sanger.ac.uk/pub/wormbase/FROZEN_RELEASES/WS140
ftp://ftp.sanger.ac.uk/pub/wormbase/WS170

Our gene tracks here are merely copies of what worm base has released.

--Hiram

Nathan Gaddis wrote:
> I have performed a tiling array analysis using the C. elegans Tiling 1.0R
> Array, which has over 3 million 25-mer probes covering the entire
> non-repetitive genome.  The probes used in this array are derived from C.
> elegans assembly ce3.  I have been trying to annotate the results of this
> analysis (Affy does not provide an annotation file) but have run into the
> problem that the annotations for both ce2 and ce4 are slightly shifted in
> certain areas relative to ce3.  This presents problems since I am trying to
> map the genome positions of the probes to specific exons.  Ideally what I
> need are the following data dumps from ce3: 1) a GTF file for the entire
> genome (track: WormBase Genes, table: sangerGene) and 2) a BED file for the
> entire genome with one BED record per exon (track WormBase Genes, table:
> sangerGene).  Is there any way to get a hold of these data.  Thanks.
> 
>  
> 
> Nathan Gaddis