<div dir="ltr"><div>Hi Irina, I have been playing with the plugin (thanks for that again!). <br></div><div><br></div><div>What I am actually interested is in the distance of the variant to the next exon-exon junction, as defined by the CDS and not by the 'absolute' bps (including UTR), which is what determines whether the NMD will act (see <a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002296">here</a>), which is what i want to detect. I was not clear enough on that, apologies.</div><div><br></div><div>In any case, what you re retrieving now is actually also interesting for other evaluations. Maybe you could include what you have now and also the coding sequence values ? Again, note that I address these calculations by my own ad hoc scripts, so consider to implement it (together with the location of the frameshift-induced stop codon mentioned before) just if you believe that it can be of interest for the community (which i think it does!) <br></div><div><br></div><div>br</div><div>d<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El lun., 4 mar. 2019 a las 18:33, David Tamborero (<<a href="mailto:david.tamborero@gmail.com">david.tamborero@gmail.com</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>thta s great, i m currently travelling but i will try it as soon as i back to the lab (and feedback you guys as appropriate)<br></div><div><br></div><div>thanks again!</div><div>d<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El vie., 1 mar. 2019 a las 16:27, Irina Armean (<<a href="mailto:iarmean@ebi.ac.uk" target="_blank">iarmean@ebi.ac.uk</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi David,</p>
<p>The <span style="box-sizing:border-box;color:rgb(36,41,46);font-family:-apple-system,system-ui,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";font-size:16px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="gmail-m_-5727380057110329055gmail-m_3538932301546639360final-path">NearestExonJB.pm plugin is now
available on github <a class="gmail-m_-5727380057110329055gmail-m_3538932301546639360moz-txt-link-freetext" href="https://github.com/Ensembl/VEP_plugins" target="_blank">https://github.com/Ensembl/VEP_plugins</a>. This
plugin reports the nearest exon junction boundary (exon id, bp
distance, start or end, exon length) within the affected
transcript.</span></p>
<p><span style="box-sizing:border-box;color:rgb(36,41,46);font-family:-apple-system,system-ui,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";font-size:16px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="gmail-m_-5727380057110329055gmail-m_3538932301546639360final-path">I hope you find it useful.<br>
</span></p>
<p><span style="box-sizing:border-box;color:rgb(36,41,46);font-family:-apple-system,system-ui,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";font-size:16px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="gmail-m_-5727380057110329055gmail-m_3538932301546639360final-path">Best regards,</span></p>
<p><span style="box-sizing:border-box;color:rgb(36,41,46);font-family:-apple-system,system-ui,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";font-size:16px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial" class="gmail-m_-5727380057110329055gmail-m_3538932301546639360final-path">Irina</span><strong class="gmail-m_-5727380057110329055gmail-m_3538932301546639360final-path" style="box-sizing:border-box;font-weight:600;color:rgb(36,41,46);font-family:-apple-system,system-ui,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol";font-size:16px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br>
</strong></p>
<div class="gmail-m_-5727380057110329055gmail-m_3538932301546639360moz-cite-prefix">On 25/02/2019 08:40, David Tamborero
wrote:<br>
</div>
<blockquote type="cite">
<div dir="auto">That s fantastic, thanks!
<div dir="auto"><br>
</div>
<div dir="auto">Have a great week</div>
<div dir="auto">D</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">El vie., 22 feb. 2019 17:48,
Irina Armean <<a href="mailto:iarmean@ebi.ac.uk" target="_blank">iarmean@ebi.ac.uk</a>> escribió:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi David,</p>
<p>Thanks for the clarification and the positive feedback
for the team. We do our best to make the desired
functionality available in due time, sometimes it's
easier/faster than other times.<br>
</p>
<p>We plan to add a VEP plugin within the next week, which
will report the nearest exon junction boundary (exon id,
bp distance, start or end, exon length) for variants in
the protein coding region, this should answer your case
and also provide some additional use cases.<br>
</p>
<p>For the case of frameshifts and premature stop codons,
they are handled more efficiently in the main VEP code and
is more complex to update quickly however we plan to cover
this use case in the near future.</p>
<p>I will come back with a mail once the plugin is in.<br>
</p>
<p>Best regards,</p>
<p>Irina<br>
</p>
<p><br>
</p>
<div class="gmail-m_-5727380057110329055gmail-m_3538932301546639360m_-16577229655441767moz-cite-prefix">On
21/02/2019 17:17, David Tamborero wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div>Hi Irina, thanks for your answer, it is always
awesome how diligent you are guys; <br>
</div>
<div><br>
</div>
<div>my wishlist:</div>
<div><br>
</div>
<div>- in my case, what i m interested in is in the
distance (nucleotides) from my variant 'within' the
exon (ie protein coding-affecting variant) to the
next exon junction. But note that other users may be
interested in other distances, as those that you
mention.</div>
<div><br>
</div>
<div>- FYI, i m interested in that info for the
variants that create preamture stop codons, so I can
estimate whether it will be likely that the
non-mediated decay is triggered (which depends on
how far it falls regarding the last junction of the
transcript). Note that --for the same reason-- I m
also interested in, given a frameshift mutation,
where the new 'cryptic' stop codon will be placed. I
currently calculate it by actually using the VEP
info that can be parsed from the HGVSp column (e.g.
p.Glu5ValfsTer5, meaning the stop codon in 5 codons
after the first 'ectopic codon' created by the
frameshift, if I remember well).</div>
<div><br>
</div>
<div>Again, I currently address both cases by my own
ad hoc scripts, but I thought that you already
'have' the info to easily output these things, which
I think it can be of interest for the community (and
surely more neat that my creepy coding!)<br>
</div>
<div><br>
</div>
<div>hope it makes sense!</div>
<div>br</div>
<div>d<br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">El jue., 21 feb. 2019
a las 17:12, Irina Armean (<<a href="mailto:iarmean@ebi.ac.uk" rel="noreferrer" target="_blank">iarmean@ebi.ac.uk</a>>)
escribió:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Dear David,</p>
<p>Thanks for the question. We currently don't have
this functionality however we can easily add the
distance to the closest exon.</p>
<p>To clarify, are you interested in getting the
distance to the nearest exon junction for the
variants only when it affects a protein coding
transcript or also when they are
upstream/downstream of genes for example?</p>
<p>Best regards,</p>
<p>Irina</p>
<p><br>
</p>
<div class="gmail-m_-5727380057110329055gmail-m_3538932301546639360m_-16577229655441767gmail-m_-7639736395750451905moz-cite-prefix">On
21/02/2019 11:09, David Tamborero wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Dear all, <br>
</div>
<div><br>
</div>
<div>is any flag (which I cannot find) so the
VEP output includes the distance of the
(coding) variant to the closest exon junction?</div>
<div><br>
</div>
<div>If not, somebody has a recommended fancy
approach to do so? (My current approach is
'just' to match with my own script the VEP
output for a given transcript with the exon
coordinates data that can be retrieved in e.g.
BioMart)</div>
<div><br>
</div>
<div>many thanks in advance!</div>
<div>d<br>
</div>
</div>
<br>
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</blockquote>
<pre class="gmail-m_-5727380057110329055gmail-m_3538932301546639360m_-16577229655441767gmail-m_-7639736395750451905moz-signature" cols="72">--
Irina Armean PhD, Bioinformatican
Ensembl Variation, EMBL-EBI, Hinxton, UK
iarmean[at]<a href="http://ebi.ac.uk" rel="noreferrer" target="_blank">ebi.ac.uk</a> | A3 - 135</pre>
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<pre class="gmail-m_-5727380057110329055gmail-m_3538932301546639360m_-16577229655441767moz-signature" cols="72">-- </pre>
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