[ensembl-dev] [SPAM] - Re: [SPAM] - Re: [SPAM] - Re: Transcript variation alleles - Email found in subject - Email found in subject - Email found in subject

[Oliver, Gavin]

Ok...

 

So as it stands the alleles I am returning are genomic and called via
variation features.  Are they always relative to the forward strand?

 

 

________________________________

From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will
McLaren
Sent: 02 February 2011 16:04
To: Oliver, Gavin
Cc: Graham Ritchie; dev at ensembl.org
Subject: [SPAM] - Re: [SPAM] - Re: [SPAM] - Re: [ensembl-dev] Transcript
variation alleles - Email found in subject - Email found in subject -
Email found in subject

 

Well yes, of course it depends on what you mean!

 

A transcript object in Ensembl represents the region of the genome that
generates the cDNA, not the mRNA itself - this is the only thing that
we'd be able to transfer the variation_feature object to, as I don't
think there is an Ensembl object representing the mRNA.

 

Will

On 2 February 2011 15:54, Oliver, Gavin <gavin.oliver at almacgroup.com>
wrote:

P.S.

 

Should it not be the other way around?

 

i.e. if the transcript originates from the same strand as the variation
feature then the alleles will be different?  As the transcript will be
the reverse complement of the strand it originated on?

 

Or have I tied my head in a knot?

 

 

 

________________________________

From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will
McLaren
Sent: 02 February 2011 15:41
To: Oliver, Gavin
Cc: Graham Ritchie; dev at ensembl.org
Subject: [SPAM] - Re: [SPAM] - Re: [ensembl-dev] Transcript variation
alleles - Email found in subject - Email found in subject

 

There is no direct method to do this (if I'm following you exactly).

 

If the transcript is on the same strand as the variation_feature (use
$vf->seq_region_strand and $transcript->seq_region_strand), then the
transcript alleles will be the same; if they are different, then you
will need to reverse complement the alleles:

 

use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);

my $new_allele_string;

 

foreach my $allele(split /\//, $vf->allele_string) {

  reverse_comp($allele);

  $new_allele_string .= $allele.'/';

}

 

$new_allele_string =~ s/\/$//;

 

We can add this functionality as $vf->transfer() if people would find it
useful.

 

Will

 

On 2 February 2011 15:27, Oliver, Gavin <gavin.oliver at almacgroup.com>
wrote:

How would I go about pulling the transcriptomic one?

 

________________________________

From: wmclaren at gmail.com [mailto:wmclaren at gmail.com] On Behalf Of Will
McLaren
Sent: 02 February 2011 15:27
To: Oliver, Gavin
Cc: Graham Ritchie; dev at ensembl.org
Subject: Re: [SPAM] - Re: [ensembl-dev] Transcript variation alleles -
Email found in subject

 

In this case, as Graham says, the alleles will be the genomic alleles,
since you are calling from a variation_feature object.

 

Will

On 2 February 2011 15:21, Oliver, Gavin <gavin.oliver at almacgroup.com>
wrote:

I'm using transcriptvariation->variation_feature->allele_string

 

________________________________


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