Hi Sim,
You can retrieve this information from the Table Browser, please see
this previously answered mailing list question:
https://lists.soe.ucsc.edu/pipermail/genome/2007-November/014951.html
From main page, click on "Tables" (in the top blue navigation bar).
After selecting a clade, genome, and assembly of your choice, set the
following:
group: Genes and Gene Prediction Tracks
track: Ensembl Genes
table: knownToEnsembl
output format: selected fields from primary and related tables
output file: enter a filename to save your results to a file, or leave
blank to display results in the browser
Click 'get output'. On the following page, select the appropriate fields
('name' for example). Scroll down, select 'kgXref' and click 'Allow
Selection From Checked Tables.' Select 'refseq' then click 'get output'.
More information on how to use the Table Browser can be found here:
http://genome.ucsc.edu/cgi-bin/hgTables#Help
Please contact us again at [email protected] if you have any further
questions.
---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
SIM Ngak Leng wrote:
> Greetings,
>
> I'm trying to find the file that maps Ensembl to RefSeq, but can't seem to
> figure out which file it is.
>
> Could you point me to the right file? If not, could you advise me on how to
> go about getting the mappings between the 2 gene annotations? Thanks in
> advance.
>
> Regards,
> Sim Ngak Leng
> Computational and Mathematical Biology 8
> Genome Institute of Singapore
>
> PS: I understand that
> (1) ccdsInfo allows us to map CCDS to Ensembl, and CCDS to RefSeq
> (2) knownToRefSeq maps known to RefSeq
> (3) knownToEnsembl maps known to Ensembl
> (4) ccdsKgMap maps ccds to Known.
> But none of them maps Ensembl and RefSeq directly. If there are mappings
> between Ensembl and RefSeq but not to CCDS and Known, they will be missed
> out...
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
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https://lists.soe.ucsc.edu/mailman/listinfo/genome
