<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Sigurjón,<div class=""><br class=""></div><div class="">unfortunately there is no straightforward way of getting overlaps with unverified motif features. We are providing GFF dumps with all motif features here <a href="ftp://ftp.ensembl.org/pub/release-99/regulation/homo_sapiens/MotifFeatures/" class="">ftp://ftp.ensembl.org/pub/release-99/regulation/homo_sapiens/MotifFeatures/</a>.<br class=""><div><br class=""></div><div>VEP does support custom annotation. However, at the moment VEP still lacks the option to create features similar to transcripts from a GFF file containing motif features. We are working on it and hopefully should support this use case in a coming release.</div><div><br class=""></div><div>If you have a chance to convert the GFF files into BED files you can use VEP’s custom annotation option for BED files: <a href="https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html" class="">https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html</a></div><div><br class=""></div><div>We also display all motif features in our browser: <a href="https://jan2020.archive.ensembl.org/Homo_sapiens/Share/0b737ea4a480564bb963aa2f4a019461?redirect=no;mobileredirect=no" class="">https://jan2020.archive.ensembl.org/Homo_sapiens/Share/0b737ea4a480564bb963aa2f4a019461?redirect=no;mobileredirect=no</a> which could be useful if you want to look up individual cases.<span class="Apple-tab-span" style="white-space:pre"> </span></div><div><br class=""></div><div><br class=""></div><div>Best wishes,</div><div>Anja</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On 12 Mar 2020, at 13:55, Sigurjón Axel Guðjónsson <<a href="mailto:Sigurjon.Gudjonsson@decode.is" class="">Sigurjon.Gudjonsson@decode.is</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi Anja,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thank you for explaining this.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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 class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Best regards,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Sigurjón<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>Dev <<a href="mailto:dev-bounces@ensembl.org" class="">dev-bounces@ensembl.org</a>><span class="Apple-converted-space"> </span><b class="">On Behalf Of<span class="Apple-converted-space"> </span></b>Anja Thormann<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>fimmtudagur, 12. mars 2020 13:12<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Ensembl developers list <<a href="mailto:dev@ensembl.org" class="">dev@ensembl.org</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ensembl-dev] Motif feature consequences discrepancy<o:p class=""></o:p></span></div></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Hi Sigurjon,<o:p class=""></o:p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">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/" style="color: purple; text-decoration: underline;" class="">post</a> gives more details on how we report motif features.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Best wishes,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">Anja<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div></div><div class=""><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">On 12 Mar 2020, at 12:53, Sigurjón Axel Guðjónsson <<a href="mailto:Sigurjon.Gudjonsson@decode.is" style="color: purple; text-decoration: underline;" class="">Sigurjon.Gudjonsson@decode.is</a>> wrote:<o:p class=""></o:p></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></span></div></div><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">Hi,<o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class=""> <o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">I am using VEP r99 to annotate i.e. rs759323910, and I notice that VEP only annotates MotifFeature ENSM00524563717 (ENSPFM0379). <o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">The web browser does hower annotate 2 MotifFeatures ENSM00524563717 (ENSPFM0588) and ENSM00489900360 (ENSPFM0379). <o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class=""> <o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">See:<o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class=""><a href="http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;v=rs759323910;vdb=variation" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;v=rs759323910;vdb=variation</span></a><o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class=""> <o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">Is there any valid reason for this discrepancy or is this a bug in VEP r99?<o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class=""> <o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">Best regards,<o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class=""> <o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">Sigurjon A. Gudjonsson<o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">Bioinformatics Group<o:p class=""></o:p></pre><pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: "Courier New";" class="">Decode Genetics<o:p class=""></o:p></pre><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class="">_______________________________________________<br class="">Dev mailing list </span><a href="mailto:Dev@ensembl.org" style="color: purple; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: rgb(149, 79, 114);" class="">Dev@ensembl.org</span></a><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class=""><br class="">Posting guidelines and subscribe/unsubscribe info:<span class="apple-converted-space"> </span></span><a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" style="color: purple; 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