<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.EmailStyle21
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="IS" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Anja,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thank you for explaining this.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Would it be possible to optionally show unverified motif features in VEP. I.e. if the relevant cell line is missing ChIP-Seq
peak data.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Sigurjón<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Dev <dev-bounces@ensembl.org>
<b>On Behalf Of </b>Anja Thormann<br>
<b>Sent:</b> fimmtudagur, 12. mars 2020 13:12<br>
<b>To:</b> Ensembl developers list <dev@ensembl.org><br>
<b>Subject:</b> Re: [ensembl-dev] Motif feature consequences discrepancy<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Sigurjon,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal">VEP only reports overlaps with 'experimentally verified’ motif features. Which means those motif features fully overlap with a relevant ChIP-Seq peak. On the website we are still showing overlaps with unverified motif features. This will
be updated for next release 100 when we are only going to show overlaps with 'experimentally verified’ motif features. Our blog <a href="http://www.ensembl.info/2018/10/15/new-ensembl-motif-features/">post</a> gives more details on how we report motif features.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best wishes,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Anja<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 12 Mar 2020, at 12:53, Sigurjón Axel Guðjónsson <<a href="mailto:Sigurjon.Gudjonsson@decode.is">Sigurjon.Gudjonsson@decode.is</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
</div>
<pre>Hi,<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>I am using VEP r99 to annotate i.e. rs759323910, and I notice that VEP only annotates MotifFeature ENSM00524563717 (ENSPFM0379). <o:p></o:p></pre>
<pre>The web browser does hower annotate 2 MotifFeatures ENSM00524563717 (ENSPFM0588) and ENSM00489900360 (ENSPFM0379). <o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>See:<o:p></o:p></pre>
<pre><a href="http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;v=rs759323910;vdb=variation"><span style="color:#954F72">http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;v=rs759323910;vdb=variation</span></a><o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Is there any valid reason for this discrepancy or is this a bug in VEP r99?<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Best regards,<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Sigurjon A. Gudjonsson<o:p></o:p></pre>
<pre>Bioinformatics Group<o:p></o:p></pre>
<pre>Decode Genetics<o:p></o:p></pre>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
Dev mailing list </span><a href="mailto:Dev@ensembl.org"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">Dev@ensembl.org</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
Posting guidelines and subscribe/unsubscribe info:<span class="apple-converted-space"> </span></span><a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
Ensembl Blog:<span class="apple-converted-space"> </span></span><a href="http://www.ensembl.info/"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">http://www.ensembl.info/</span></a><o:p></o:p></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</body>
</html>