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Covert coordinates of a specific chromosome region from Grch38 to grch37?
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17 months ago
DanielC • 80
Canada

Dear Friends,

I have a specific region on a chromosome on grch38 for which I want the corresponding coordinates in grch37. I know how to do it using liftover but, trying to do it using Ensembl Perl API. Anyone who has done it before? Can you please share?

Thanks, DK

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I believe you need the transform() and transfer() methods, see the Ensembl Core API Tutorial.

There is also a Web interface for simpler / smaller tasks: https://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core

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Thanks, I am looking for standalone method. Sp API is a good approach. I already have gone through the tutorial, just wondering if there is any example describing this?

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I am using Ensembl Perl API but when performing this step, I get this error:

use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(-host => 'ensembldb.ensembl.org',-user => 'anonymous');
Can't call method "load_registry_from_db" on an undefined value at (eval 19)[/usr/share/perl5/perl5db.pl:646] line 2.

Any idea how to resolve this issue? thanks

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Ok, I resolved this issue, but one question remains:

When using transform() and transfer(), how do we know if we are transferring coordinates from grch38 to grch37? In the tutorial there is no mention of such conversion. Any comments?

Thanks

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