Hi Alex,
Thanks for fixing that! I'll make sure to keep my eye out for other bugs.
As a future feature request,
It would be really great if we could also get start phase, and end phase for
each exon like the ensembl output seen here.
http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000139618;r=13:32889611-32973805;t=ENST00000380152
John Pan
[email protected]
From: Arek Kasprzyk [mailto:[email protected]]
Sent: Friday, September 14, 2012 7:24 AM
To: John Pan
Cc: [email protected]; Francis Ouellette ([email protected])
Subject: Re: [BioMart Users] Missing Phase Information in Biomart 0.8
Hi John,
we have now restored the phase information in the 08 BioPortal
Please let us know if there are any more problems
a
On Wed, Aug 29, 2012 at 9:40 PM, John Pan
<[email protected]<mailto:[email protected]>> wrote:
Hello,
I was directed here by the Ensembl Helpdesk.
I wanted to ask about a difference in exportable information found between
BioMart 0.8 portal and Biomart 0.7 portal
Under the structure tab for exons it is possible to export Phase information in
version 0.7
However, in Biomart 0.8 it is no longer possible.
Was this removed for a reason? A mis-configuration? Should I be wary of using
the phase information in 0.7?
Additionally, if it's possible I would suggest the feature of being able to
export start phase and end phase as seen in the Exon link in the Ensembl Browser
Example:
http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000139618;r=13:32889611-32973805;t=ENST00000380152
While it is possible to calculate start and end phase using exon rank, exon
phase and exon phase of the next exon it is difficult to judge whether a
hypothetical alternative splicing event would have compatible exon phase to
maintain an in-correct frame transcript
Thank you,
John Pan | Bioinformatics group
Genomic Health | 301 Penobscot Dr., Redwood City, CA 94063
Direct - ' 1-650-569-5614| *
[email protected]<mailto:[email protected]>
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