[ensembl-dev] Converting genomic coordinates to transcript/exon etc

Oliver, Gavin gavin.oliver at almacgroup.com
Tue Nov 9 09:25:29 GMT 2010


My original coordinates are a subset of the full transcript - is there a
way of converting these coordinates to the transcript coordinates?

E.g. 175 - 300

?

-----Original Message-----
From: Will Spooner [mailto:whs at eaglegenomics.com] 
Sent: 08 November 2010 17:39
To: Oliver, Gavin
Cc: dev at ensembl.org
Subject: Re: [ensembl-dev] Converting genomic coordinates to
transcript/exon etc

It's giving you the cdna coordinates of ENST00000297564 for your region
100890372..100905895. There are three exons (by the look of it), 1..29,
30..174, 175..303 and 304..425, and their corres[ponding genomic
locations. 

Will



On 8 Nov 2010, at 17:28, Oliver, Gavin wrote:

> Hi Will.
> 
> Thanks.
> 
> I'm not certain what the method is doing though.
> 
> I did this: 
> 
> 
> my $transcript =
> $transcript_adaptor->fetch_by_stable_id('ENST00000297564');
> my $trmapper = Bio::EnsEMBL::TranscriptMapper->new($transcript);
> 
> my  @coords = $trmapper->genomic2cdna( 100890372, 100905895, -1 );
> 
> foreach my $thing (@coords) {
>        print $thing->start."\t".$thing->end."\n";
> }
> 
> And get the following:
> 
> 1       29
> 100904281       100905866
> 30      174
> 100899847       100904135
> 175     303
> 100890494       100899717
> 304     425
> 
> The method doesn't seem to do anything with my input coordinates.
> 
> But then I could well be missing something :)
> 
> Gavin
> 
> -----Original Message-----
> From: Will Spooner [mailto:whs at eaglegenomics.com] 
> Sent: 08 November 2010 16:29
> To: Oliver, Gavin
> Cc: dev at ensembl.org
> Subject: Re: [ensembl-dev] Converting genomic coordinates to
> transcript/exon etc
> 
> Hi Gavin,
> 
> Take a look at Bio::EnsEMBL::TranscriptMapper;
> 
> my $trmapper = Bio::EnsEMBL::TranscriptMapper->new($transcript);
>  @coords = $trmapper->cdna2genomic( 123, 554 );
>  @coords = $trmapper->genomic2cdna( 141, 500, -1 );
>  @coords = $trmapper->genomic2cds( 141, 500, -1 );
>  @coords = $trmapper->pep2genomic( 10, 60 );
>  @coords = $trmapper->genomic2pep( 123, 400, 1 );
> 
> Where @coords are Bio::EnsEMBL::Mapper::Coordinate and Gap objects.
> 
> Best,
> 
> Will
> 
> 
> On 8 Nov 2010, at 16:04, Oliver, Gavin wrote:
> 
>> Hi all,
>> 
>> Using the funcgen API, if I know a probe feature maps to exon 2 of
> transcript A and the genomic coordinates are chromosome X bases
> 99-110...
>> 
>> ..how do I convert the genomic coordinates to transcript coordinates?
>> 
>> I have been reading the docs but I'm lost to be honest.
>> 
>> Gavin
>> 
>> 
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
> 
> --
> William Spooner
> whs at eaglegenomics.com
> http://www.eaglegenomics.com
> 
> 
> 
> 
> The contents of this message and any attachments to it are
confidential and may be legally privileged. If you have received this
message in error, you should delete it from your system immediately and
advise the sender.
> 
> Almac Group (UK) Limited, registered no. NI061368.  Almac Sciences
Limited, registered no. NI041550.  Almac Discovery Limited, registered
no. NI046249.  Almac Pharma Services Limited, registered no. NI045055.
Almac Clinical Services Limited, registered no. NI041905.  Almac
Clinical Technologies Limited, registered no. NI061202.  Almac
Diagnostics Limited, registered no. NI043067.  All preceding companies
are registered in Northern Ireland with a registered office address of
Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK.  
> 
> Almac Sciences (Scotland) Limited, registered in Scotland no.
SC154034. 
> 
> Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac
Diagnostics LLC are Delaware limited liability companies and Almac Group
Incorporated is a Delaware Corporation.  More information on the Almac
Group can be found on the Almac website: www.almacgroup.com
> 
> 

--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com







More information about the Dev mailing list