[Biopython] 1. Converting transcript coordinates to genome coordinates

[Peter Thorpe]

Hi Micheal,

I think this is a too specific problem to trust someone else's code for.
However, You could BLAT (https://genome.ucsc.edu/FAQ/FAQblat.html) you
transcripts against the genome, then convert the output to GFF.

Are the exons not defined in a genomic GFF3? If you want to know which exon
your coordinate of interest falls into, you could use *bedtools intersect*.
This could be used to find the region of interest and which exon it
overlaps with (you will have to format an exon coordinate GFF) and a
region_of_interest.gff for this.

 bedtools intersect: (
http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html)

    -wao Write amounts of overlap for all features.

    bedtools intersect -wao -a genome.gff -b region_of_interest.gff >
results.txt

I hope that helps.

Cheers,

Pete Thorpe


On 5 July 2017 at 13:00, <biopython-request at mailman.open-bio.org> wrote:

> Send Biopython mailing list submissions to
>         biopython at mailman.open-bio.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://mailman.open-bio.org/mailman/listinfo/biopython
> or, via email, send a message with subject or body 'help' to
>         biopython-request at mailman.open-bio.org
>
> You can reach the person managing the list at
>         biopython-owner at mailman.open-bio.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Biopython digest..."
>
>
> Today's Topics:
>
>    1. Converting transcript coordinates to genome coordinates
>       (Michiel de Hoon)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 5 Jul 2017 10:04:14 +0000 (UTC)
> From: Michiel de Hoon <mjldehoon at yahoo.com>
> To: Biopython Mailing List <biopython at biopython.org>
> Subject: [Biopython] Converting transcript coordinates to genome
>         coordinates
> Message-ID: <1455479474.5720626.1499249054600 at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
> Does anybody have some code to convert transcript coordinates to genome
> coordinates?
> I have the position of a nucleotide along a transcript, and the genome
> coordinates of the start and end of each exon in the transcript, and I
> would like to find the position of the nucleotide in genome
> coordinates.Ideally, I am looking for some code that can find the genome
> coordinates of a sequence of nucleotides.For example, if these are the
> exons:exon1? 10000 10030exon2? 10050 10080and a nucleotide sequence
> starting at position 20 and ending at position 50 in transcript coordinates,
> then I am looking for the genome coordinates (10020,10030), (10050,10070).
> Thanks,-Michiel
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <http://mailman.open-bio.org/pipermail/biopython/
> attachments/20170705/896e45c0/attachment-0001.html>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
> ------------------------------
>
> End of Biopython Digest, Vol 175, Issue 1
> *****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20170705/ce1d7d03/attachment.html>