[ensembl-dev] mm10-style chromosome names

Sergei Manakov siarheimanakov at gmail.com
Mon Sep 10 10:27:36 BST 2012


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




-- 
Sergei (Siarhei Manakou) Manakov

California Institute of Technology

+1 626 395 3593




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