[ensembl-dev] using the GRCh37 coordinate system inside current ensembl human core

[Emily Perry]

Hi Vivek

You can use the e79 API with port 3337 to connect to the up-to-date 
GRCh37 annotation.

All the best

Emily

On 17/04/2015 11:56, Vivek Iyer wrote:
> Hi all,
>
> I have a set of genomic positions in GRCh37 (corresponding to virus insertion sites, which were found by someone else, mapping genomic sequence to the GRCh37 assembly). I am simply annotating these insertions sites with human ensembl genes - using some suitable flanking distance.
>
> I think I have two choices, which seem slightly different:
>
> (1) connect with my API to  ensembl release 75 - the last GRCh37 release - and do everything inside that universe. Load slices given by my reference positions, read off the genes, bob’s your uncle.
>
> (2) connect with the API to the current ensembl release (79, GRCh38).
> Load slices in coordinate_system = chromosome, version = ‘GRCh37’ around my reference positions.
> Then read off genes on those slices as I need.
>
> So I think the difference is that (2) will get me annotations actually done on GRCh38 ‘pulled back’ into GRCh37, whereas (1) will get me annotations actually done on GRCh37 from end-to-end. Is this correct? I’d prefer to use (2) unless someone tells me that’s a baaad idea.
>
> Thanks,
>
> Vivek
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-- 
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK