<div dir="ltr"><div><div><div>Hi Micheal,<br><br></div>I think this is a too specific problem to trust someone else's code for. However, You could BLAT (<a href="https://genome.ucsc.edu/FAQ/FAQblat.html">https://genome.ucsc.edu/FAQ/FAQblat.html</a>) you transcripts against the genome, then convert the output to GFF.<br><br>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 <i>bedtools intersect</i>. 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.<br><br> bedtools intersect: (<a href="http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html">http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html</a>)<br> <br> -wao Write amounts of overlap for all features.<br> <br> bedtools intersect -wao -a genome.gff -b region_of_interest.gff > results.txt<br><br></div><div>I hope that helps.<br></div><div><br></div>Cheers,<br><br></div>Pete Thorpe<br><div><div><br><br><div><div class="gmail_extra"><div class="gmail_quote">On 5 July 2017 at 13:00, <span dir="ltr"><<a href="mailto:biopython-request@mailman.open-bio.org" target="_blank">biopython-request@mailman.open-bio.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send Biopython mailing list submissions to<br>
<a href="mailto:biopython@mailman.open-bio.org">biopython@mailman.open-bio.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biopython" rel="noreferrer" target="_blank">http://mailman.open-bio.org/<wbr>mailman/listinfo/biopython</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:biopython-request@mailman.open-bio.org">biopython-request@mailman.<wbr>open-bio.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:biopython-owner@mailman.open-bio.org">biopython-owner@mailman.open-<wbr>bio.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Biopython digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Converting transcript coordinates to genome coordinates<br>
(Michiel de Hoon)<br>
<br>
<br>
------------------------------<wbr>------------------------------<wbr>----------<br>
<br>
Message: 1<br>
Date: Wed, 5 Jul 2017 10:04:14 +0000 (UTC)<br>
From: Michiel de Hoon <<a href="mailto:mjldehoon@yahoo.com">mjldehoon@yahoo.com</a>><br>
To: Biopython Mailing List <<a href="mailto:biopython@biopython.org">biopython@biopython.org</a>><br>
Subject: [Biopython] Converting transcript coordinates to genome<br>
coordinates<br>
Message-ID: <<a href="mailto:1455479474.5720626.1499249054600@mail.yahoo.com">1455479474.5720626.<wbr>1499249054600@mail.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all,<br>
Does anybody have some code to convert transcript coordinates to genome coordinates?<br>
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,<br>
then I am looking for the genome coordinates (10020,10030), (10050,10070).<br>
Thanks,-Michiel<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://mailman.open-bio.org/pipermail/biopython/attachments/20170705/896e45c0/attachment-0001.html" rel="noreferrer" target="_blank">http://mailman.open-bio.org/<wbr>pipermail/biopython/<wbr>attachments/20170705/896e45c0/<wbr>attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Subject: Digest Footer<br>
<br>
______________________________<wbr>_________________<br>
Biopython mailing list - <a href="mailto:Biopython@mailman.open-bio.org">Biopython@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biopython" rel="noreferrer" target="_blank">http://mailman.open-bio.org/<wbr>mailman/listinfo/biopython</a><br>
<br>
------------------------------<br>
<br>
End of Biopython Digest, Vol 175, Issue 1<br>
******************************<wbr>***********<br>
</blockquote></div><br></div></div></div></div></div>