[ensembl-dev] mm10-style chromosome names

Magali mr6 at ebi.ac.uk
Mon Sep 10 10:40:26 BST 2012


Hi Sergei,

Ensembl stores synonyms for regions when these are available.
For the new mouse assembly, these would look like CM000999.2 for
chromosomes and MMCHR1_RANDOM_CTG1 for toplevel scaffolds.
You can retrieve them using the perl API using the method
get_all_synonyms on the slice object.


Hope that helps,
Magali

On 10/09/12 10:27, 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
>
>
>
>





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