[ensembl-dev] get sequence from different build

Hiram Clawson hiram at soe.ucsc.edu
Fri Sep 24 18:25:25 BST 2010


FYI:  for your example position: chr11:60001-70001 in GRCh37
this translates to position: chr11:50001-60001 in build 36
All of this is on the exact same contig in both assemblies: AC069287.7

Positions will not always translate correctly.  GRCh37 and build
36 do not always use the same contigs everywhere.

--Hiram

ian Longden wrote:
> Ah yes i did my test on another region where there was sequence:-
> here is the full code and example:-
> 
> -----------------------------------------------------------------------------------------------------
> use Bio::EnsEMBL::Registry;
> my $s = 'Human';      # species-name
> my $r = 'chromosome'; # slice region
> my $c = 11;           # chromosome
> 
> 
> #my $p = 123000000;    # position
> my $p = 60001;

> ------------------------------------------------------------------------------------------------
> Giving:-
> 
> Seq for 37:-
> GAATTCTACATTAGAAAAATA
> Seq for 36:-
> AGGCAGAGGTCAAAGTGAGCC




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