[ensembl-dev] get sequence from different build
mailsvl at fastmail.fm
mailsvl at fastmail.fm
Thu Sep 16 12:54:10 BST 2010
Hi,
How can I get a slice from a different build then the default? When I
try to compare GCRh37 and NCBI36 I keep getting the same sequences (from
GCRh37), no matter what region I try.
The code I use is from:
http://www.ensembl.org/info/docs/api/core/core_tutorial.html
Code:
- $slice_adaptor->fetch_by_region( 'chromosome', '11', 123000000,
123000020, 'NCBI36' ); or
- $slice_adaptor->fetch_by_region( 'chromosome', '11', 123000000,
123000020, 1, 'NCBI36' );
Results when using ensembl website:
>11 dna:chromosome chromosome:NCBI36:11:123000000:123000020:1
AAGAGTCCCACCAGCTCCAGG
>11 dna:chromosome chromosome:GRCh37:11:123000000:123000020:1
TGCACTCCAGCCTGGGCAATG
Thanks,
Stef
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