[ensembl-dev] mm10-style chromosome names

[Hiram Clawson]

To see the UCSC name relationships:

mysql -hgenome-mysql.cse.ucsc.edu -ugenomep -ppassword -A \
	-e "select chrom,frag from gold;" mm10

--Hiram

On 9/10/12 2:27 AM, Sergei Manakov wrote:
> hello,
>
> After retrieving slices for chromosome and scaffolds
>
> my @slices = @{ $slice_adaptor->fetch_all('toplevel') };
>
> I get sequence region names with this command:
>
>   $slice->seq_region_name();
>
>
> UCSC genome mm10 is based on GRCm38 assembly, but they did not
> preserved names of chromosomes and scaffolds. I already e-mailed UCSC
> help to understand relationship between mm10 and GRCm38 nomenclature,
> but so far I have no reply from them.
>
> Does, by any chance, Ensembl have this information somewhere? If so,
> what is the way to retrieve it?
>
>
> thanks,
> Sergei