[ensembl-dev] retrieving sequence data from previous assemblies using fetch_by_region method

[Andy Yates]

Hi Duarte,

You can access GRCh37 from ensembldb.ensembl.org port number 3337. Ensembl databases currently only hold the contigs and assembly for a single assembly. That's why when you try to get sequence for GRCh37 in the GRCh38 database you get N's back

Hope this helps,

Andy

------------
Andrew Yates - Ensembl Support Coordinator
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On 6 Oct 2014, at 17:23, Duarte Molha <duartemolha at gmail.com> wrote:

> Dear developers
> 
> I have the latest API downloaded and I would want to create a scritp that could retrieve sequence information from a specified assembly
> 
> so I have made a script that tries to accomplish this:
> 
> so ...assuming this coordinates:
> 
> chr: 5
> from: 112043202
> to: 112046226
> strand = 1
> assembly = GRCh38
> 
>     my $slice = $slice_adaptor->fetch_by_region( 'chromosome', $chrom, $from, $to, $strand, $assembly );
> 
> 
>         $seq        = $slice->seq();
> 
> I can retrieve the dna sequence:
> 
> >CHR5-112043202-112046226       chr5:112043202-112046226
> AGTATATAATCACAT..............CTAAAAGCAAACA
> 
> 
> However, if I give it the variables:
> 
> chr: 5
> from: 112043202
> to: 112046226
> strand = 1
> assembly = GRCh37 or NCBI36
> 
> i get :
> 
> >CHR5-112043202-112046226       chr5:112043202-112046226
> NNNNNNNNN.........NNNNNNNNNNNNNNNN
> 
> 
> How can I get the correct underlying sequence?
> 
> Best regards
> 
> Duarte
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