[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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