[ensembl-dev] Some RefSeq transcripts seem broken

João Eiras joao.eiras at gmail.com
Tue Sep 27 12:57:44 BST 2016


Hi.

Thanks for the reply. But I might not have been clear enough.

This is how the plugin looks like

sub run {
my ($self, $tva) = @_;
return {reference => $tva->transcript_variation->_peptide};
}

As you can see, it accesses _peptide which is the wild type sequence
(I hope, I got that line from the ProteinSeqs plugin).

So, regardless of whether the variant affects the transcript or, I'm
accessing the wild type sequence... right ?

I used that variant (which is a frameshift) as an example, but could
just as well do

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr5 38300282 . GTC AAA 5000 . . .

the point of the variant it just to access the transcript (since I
don't know how to query the VEP database directly).

VEP will then report three annotations in transcripts
ENSMUST00000063136, ENSMUST00000114099 and NM_172709.3. The reference
sequence for transcripts ENSMUST00000114099 and NM_172709.3 should be
the same, but they aren't.

So, I'm concerned that the refseq transcripts are not being correctly stored.

Thank you.




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