[BioMart Users] Transcripts and the position of coding fractions of exons

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[BioMart Users] Transcripts and the position of coding fractions of exons

Inigo Martincorena
Hi,

I have been trying to use BioMart to obtain a list of all the protein
coding transcripts of the current version of the human genome. In
particular, I am interested in the start and end position of all exons,
but excluding non-coding exonic sequences (i.e. excluding UTRs).

What is the easier way of obtaining this? Or should I use Ensembl API?

So far I have retrieved all exonic starts and ends from BioMart (Exon
Start (bp)...), but these include UTRs. Combining these coordinates with
other information from BioMart I have managed to get what I wanted after
quite a bit of coding. But I was wondering whether I was missing an
easier way of getting this information directly from BioMart.

Thanks,
Inigo


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 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
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Re: [BioMart Users] Transcripts and the position of coding fractions of exons

Rhoda Kinsella
Hi Inigo
Please forward your query to [hidden email] and we will be able to help you.
Regards
Rhoda


On 31 Jan 2013, at 11:45, Inigo Martincorena <[hidden email]> wrote:

> Hi,
>
> I have been trying to use BioMart to obtain a list of all the protein coding transcripts of the current version of the human genome. In particular, I am interested in the start and end position of all exons, but excluding non-coding exonic sequences (i.e. excluding UTRs).
>
> What is the easier way of obtaining this? Or should I use Ensembl API?
>
> So far I have retrieved all exonic starts and ends from BioMart (Exon Start (bp)...), but these include UTRs. Combining these coordinates with other information from BioMart I have managed to get what I wanted after quite a bit of coding. But I was wondering whether I was missing an easier way of getting this information directly from BioMart.
>
> Thanks,
> Inigo
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD



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Re: [BioMart Users] Transcripts and the position of coding fractions of exons

Syed Haider-4
In reply to this post by Inigo Martincorena
Inigo,

To get the start/end of exons from BioMart is straight forward,
however, you need to subtract the UTRs from the first coding exon and
last coding exon - yes, you need to post-process these on your end as
this is *not* available pre-computed.

Syed

On 31 January 2013 11:45, Inigo Martincorena <[hidden email]> wrote:

> Hi,
>
> I have been trying to use BioMart to obtain a list of all the protein coding
> transcripts of the current version of the human genome. In particular, I am
> interested in the start and end position of all exons, but excluding
> non-coding exonic sequences (i.e. excluding UTRs).
>
> What is the easier way of obtaining this? Or should I use Ensembl API?
>
> So far I have retrieved all exonic starts and ends from BioMart (Exon Start
> (bp)...), but these include UTRs. Combining these coordinates with other
> information from BioMart I have managed to get what I wanted after quite a
> bit of coding. But I was wondering whether I was missing an easier way of
> getting this information directly from BioMart.
>
> Thanks,
> Inigo
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited,
> a charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE. _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users