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

[vvi]

Thanks. 

I was hoping for an explanation of the GRCh37 coord system 'lurking'
inside the mapping tables in port 5306 v79 database, but this also works
:-) 

Cheers 

Vivek 

On 2015-04-17 12:48, Emily Perry wrote: 

> 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 _______________________________________________ Dev mailing list Dev at ensembl.org Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev [1] Ensembl Blog: http://www.ensembl.info/ [2]
> 
> -- 
> 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
> 
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