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<p>Hi,</p>
<p>Did you have a look at <a class="moz-txt-link-freetext" href="https://mutalyzer.nl">https://mutalyzer.nl</a> ? There is a position
converter in there.</p>
<p>Best,</p>
<p>Gerard<br>
</p>
<br>
<div class="moz-cite-prefix">On 05/07/17 12:04, Michiel de Hoon
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:1455479474.5720626.1499249054600@mail.yahoo.com">
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<div id="yui_3_16_0_ym19_1_1499248527573_10166">Dear all,</div>
<div id="yui_3_16_0_ym19_1_1499248527573_9990"><br>
</div>
<div id="yui_3_16_0_ym19_1_1499248527573_9991">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.</div>
<div id="yui_3_16_0_ym19_1_1499248527573_10091">Ideally, I am
looking for some code that can find the genome coordinates of
a sequence of nucleotides.</div>
<div id="yui_3_16_0_ym19_1_1499248527573_10145">For example, if
these are the exons:</div>
<div id="yui_3_16_0_ym19_1_1499248527573_10146">exon1 10000
10030</div>
<div dir="ltr" id="yui_3_16_0_ym19_1_1499248527573_10101">exon2
10050 10080</div>
<div dir="ltr" id="yui_3_16_0_ym19_1_1499248527573_10147">and a
nucleotide sequence starting at position 20 and ending at
position 50 in transcript coordinates,<br>
</div>
<div dir="ltr" id="yui_3_16_0_ym19_1_1499248527573_10148">then I
am looking for the genome coordinates (10020,10030),
(10050,10070).</div>
<div dir="ltr" id="yui_3_16_0_ym19_1_1499248527573_10157"><br>
</div>
<div dir="ltr" id="yui_3_16_0_ym19_1_1499248527573_10158">Thanks,</div>
<div dir="ltr" id="yui_3_16_0_ym19_1_1499248527573_10198">-Michiel<br>
</div>
</div>
<br>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Gerard C.P. Schaafsma
Protein Structure and Bioinformatics Group
Dept. of Experimental Medical Science
Lund University
BMC B13, Hs 66
221 84 Lund
Sweden
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