<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">Do you mean this ?<br><div><img 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alt="" height="73" width="872"><br></div><br><div>However, when I look into the MT sequence in path/to/77_GRCh37/Homo_sapiens.GRCh37.77.dna.primary_assembly.fa, the length of this MT sequence is 16569bp. <br>While the length of MT sequence in hg19 is 16572bp.<br><br>Emma<br></div><div style="position:relative;zoom:1"></div><div id="divNeteaseMailCard"></div><br>At 2016-07-07 16:53:40, "Will McLaren" <wm2@ebi.ac.uk> wrote:<br> <blockquote id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><div dir="ltr">Yes, you should make sure always that you match the assembly used to call your variants with the assembly version in VEP.<div><br></div><div>Typically you will find this information in the header of the VCF generated by your variant caller.</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 7 July 2016 at 09:45, cy_jiang <span dir="ltr"><<a href="mailto:cy_jiang@126.com" target="_blank">cy_jiang@126.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Thank you very much for your quick response!<br>Does it mean that other chromosome may exists the same problem if the reference we use is GRCh37 and VEP version 77?<br><br>Thanks, <br>Emma<br></div><div><div class="h5"><br><br><br><br><div style="zoom:1"></div><div></div><br>At 2016-07-07 16:36:33, "Will McLaren" <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:<br> <blockquote style="PADDING-LEFT:1ex;MARGIN:0px 0px 0px 0.8ex;BORDER-LEFT:#ccc 1px solid"><div dir="ltr">Ensembl, and VEP, switched to GRCh38 by default from release 76 onwards.<div><br></div><div>GRCh37 is still available as a database connection or cache download, but the default is to use GRCh38.</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 7 July 2016 at 09:13, cy_jiang <span dir="ltr"><<a href="mailto:cy_jiang@126.com" target="_blank">cy_jiang@126.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Hi Will,<br>I am also interested in this problem. <br><br></div>It seems that this is based on GRCh38. <br><span><div>$ echo "MT 4249 . C T" | perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -data -force -pick -check_ref -fields HGVSc,HGVSp -o stdout -hgvs | grep -v #</div></span><div><span>ENST00000361390.2:c.943C>T ENSP00000354687.2:p.Pro315Ser<br><br></span>I look into this position(chrM:4249) in UCSC Genome Browser on Human Feb. 2009 (GRCh37/hg19) Assembly. It turns out that the base at this position is T not C.<br>When changing it to GRCh38, it changes to C.<br><br>As far as I am can remember, <span style="color:rgb(0,0,0);background-color:rgba(0,0,0,0)"></span><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5">VEP version 77 is based on GRCh37. Did I miss something there?<br><br>Emma<br></span></div><div><div><br><br><br><div style="zoom:1"></div><div></div><br>At 2016-07-07 10:02:52, "ÁÖÇí·Ò" <<a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a>> wrote:<br> <blockquote style="PADDING-LEFT:1ex;MARGIN:0px 0px 0px 0.8ex;BORDER-LEFT:#ccc 1px solid"><div dir="ltr">Dear Will,<div>Thank you so much. It do help me a lot, I have find out the bug and trying to solve, thanks!</div><div><br></div><div>Best Regard!</div><div>Lin</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-07-06 18:23 GMT+08:00 Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">The reference allele is incorrect in your input. If you specify --check_ref, VEP will warn you that the allele is wrong (and tell you what the correct allele is) and ignore that input:<div><br></div><div><div>$ echo "MT 4249 . T C" | perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --database --force --check_ref</div><div>2016-07-06 11:18:22 - Reading input from STDIN (or maybe you forgot to specify an input file?)...</div><div>2016-07-06 11:18:22 - Starting...</div><div>2016-07-06 11:18:22 - Detected format of input file as vcf</div><div><br></div><div>WARNING: Specified reference allele T does not match Ensembl reference allele C on line 1</div><div>2016-07-06 11:18:22 - Wrote stats summary to variant_effect_output.txt_summary.html</div><div>2016-07-06 11:18:22 - See variant_effect_output.txt_warnings.txt for details of 1 warnings</div><div>2016-07-06 11:18:22 - Finished!</div></div><div><br></div><div>Here's the HGVS output with the correct input (assuming that the ref/alts are switched):</div><div><br></div><div>$ echo "MT 4249 . C T" | perl <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -data -force -pick -check_ref -fields HGVSc,HGVSp -o stdout -hgvs | grep -v #</div><div>ENST00000361390.2:c.943C>T ENSP00000354687.2:p.Pro315Ser</div><div><br></div><div>Regards</div><span><font color="#888888"><div><br></div><div>Will</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On 6 July 2016 at 10:38, ÁÖÇí·Ò <span dir="ltr"><<a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello Will,<div>Thanks for you help. I have try the two method you give, but it doesn't work. Reference allele has no problem, so as "MT". If there have any other solution£¿</div><div><br></div><div>Best regard!</div><div>Lin</div></div><div class="gmail_extra"><div><div><br><div class="gmail_quote">2016-07-04 16:25 GMT+08:00 Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello Lin,<div><br></div><div>There is a problem with your input - the reference allele that you have specified does not match the reference genome sequence. You can have VEP check your input for this issue by adding --check_ref to your command line.</div><div><br></div><div>You should also use "MT" to refer to the mitochondrial chromosome in place of "M".</div><div><br></div><div>Regards</div><span><font color="#888888"><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On 4 July 2016 at 03:53, <a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a> <span dir="ltr"><<a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>
<div><span></span>Dear <span style="font-size:10.5pt;line-height:1.5;background-color:window">Thomas,</span></div><div>Thanks for your reply, it has help me so much. </div><div><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5">Now, I have another confused, I hope you can help me understand this.</span> </div><div><span style="color:rgb(0,0,0);background-color:rgba(0,0,0,0)">I am using </span><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5">ensembl-tools-release-77 now, when I use VEP to </span><span style="color:rgb(0,0,0);background-color:rgba(0,0,0,0)">annotate</span><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5"> the variants in </span><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5">mitochondria, some has the result of </span><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5">HGVSp but not have </span><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5">HGVSc (like the follow </span><span style="font-family:'Microsoft YaHei';font-size:13px;line-height:normal;white-space:nowrap;background-color:window">printscreen</span><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5">), it may be quiet strange. Then I use the VEP online to try again, but it has no result of </span><span style="font-size:10.5pt;line-height:1.5;background-color:window">HGVSc and </span><span style="font-size:10.5pt;line-height:1.5;background-color:window">HGVSp. I wonder what make this result appear.</span></div><div><span style="color:rgb(0,0,0);background-color:rgba(0,0,0,0)"> </span><img src="cid:5cd329b1$1$155c4aa3d06$Coremail$cy_jiang$126.com" style="font-size:10.5pt;line-height:1.5;background-color:window" border="0"></div><div><span style="color:rgb(0,0,0);background-color:rgba(0,0,0,0)"> </span><img src="cid:2b565313$2$155c4aa3d06$Coremail$cy_jiang$126.com" style="font-size:10.5pt;line-height:1.5;background-color:window" border="0"><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5"> </span></div><div><span style="background-color:rgba(0,0,0,0);font-size:10.5pt;line-height:1.5">Hope to hear form you.</span></div><div><span style="font-size:10.5pt;line-height:1.5;background-color:window"><br></span></div><div><span style="font-size:10.5pt;line-height:1.5;background-color:window">Yours sincerely,</span></div><div><span style="font-size:10.5pt;line-height:1.5;background-color:window">Lin</span></div><br><blockquote style="margin-top:0px;margin-bottom:0px;margin-left:0.5em"><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"><div style="PADDING-RIGHT:8px;PADDING-LEFT:8px;FONT-SIZE:12px;FONT-FAMILY:tahoma;COLOR:#000000;BACKGROUND:#efefef;PADDING-BOTTOM:8px;PADDING-TOP:8px"><div><b>From:</b> <a href="mailto:maurel@ebi.ac.uk" target="_blank">Thomas Maurel</a></div><div><b>Date:</b> 2016-06-28 17:30</div><div><b>To:</b> <a href="mailto:dev@ensembl.org" target="_blank">Ensembl developers list</a></div><div><b>Subject:</b> Re: [ensembl-dev] different between eGenetics and GNF/Atlas</div></div></div><div><div><div><div>Dear Lin,<div><br></div><div>I am afraid that this data was retired in Ensembl release 76. These might not match as the data is coming from two different sources:</div><div><br></div><span>GNF/Atlas data came to us via the Gene Expression Atlas project at EMBL-EBI.<br><br></span><a href="http://www.ebi.ac.uk/gxa/" target="_blank">http://www.ebi.ac.uk/gxa/</a><span><br><br>The GNF/Atlas data was published by the Genomics Institute of the Novartis Research Foundation:<br> <br></span><a href="http://www.gnf.org/technology/organismal/gene-expression-core.htm" target="_blank">http://www.gnf.org/technology/organismal/gene-expression-core.htm</a><span><br> <br>The eGenetics database uses Expressed Sequence Tags (ESTs) annotated with eVOC ontology terms by SANBI (South African National Bioinformatics Institute). More information below.<br><br></span><a href="http://www.ncbi.nlm.nih.gov/pubmed/12799354" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/12799354<br></a><a href="http://www.sanbi.ac.za/" target="_blank">http://www.sanbi.ac.za/</a><div><span><br></span></div><div><span>Hope this helps,</span></div><div><span>Best Regards,</span></div><div><span>Thomas<br><blockquote type="cite" style="margin-top:0px">On 28 Jun 2016, at 03:04, <a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a> wrote:<br><br>Dear Sirs,<br>I'm using biomart to filter a series of genes which are specifically expressed in the brain. In biomart there are two such filters, 'eGenetics/SANBI EST anatomical system data' and 'GNF/Atlas organism part', however, the results of these two filters don't match. I searched for it at biomart help but i couldn't find anything about this. Can anybody help me to understand the difference of these two filters?<br>I am looking forward to hearing from you.<br><br>Yours sincerely,<br>Lin<br><br>Qiongfen Lin<br>South China Normal University<br>TEL: <a href="tel:%2B8615118845463" value="+8615118845463" target="_blank">+8615118845463</a>| Mail : <a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a><br> <br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br></blockquote><br><div>--<br>Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<br>European Molecular Biology Laboratory<br>Wellcome Trust Genome Campus<br>Hinxton<br>Cambridge CB10 1SD<br>United Kingdom<br></div><br></span></div></div></div></div></div></blockquote>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br></div></div><div data-smartmail="gmail_signature"><div dir="ltr"><p><font face="΢ÈíÑźÚ, sans-serif">Arron Lin</font></p><p><font face="΢ÈíÑźÚ, sans-serif">BGI Research Institute</font></p><p><font face="΢ÈíÑźÚ, sans-serif">Email: <a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a></font></p><p><font face="΢ÈíÑźÚ, sans-serif"></font></p><p><font face="΢ÈíÑźÚ, sans-serif">Beishan Industrial Zone| Yantian District| Shenzhen 518083</font></p></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div data-smartmail="gmail_signature"><div dir="ltr"><p><font face="΢ÈíÑźÚ, sans-serif">Arron Lin</font></p><p><font face="΢ÈíÑźÚ, sans-serif">BGI Research Institute</font></p><p><font face="΢ÈíÑźÚ, sans-serif">Email: <a href="mailto:qiongfen0@gmail.com" target="_blank">qiongfen0@gmail.com</a></font></p><p><font face="΢ÈíÑźÚ, sans-serif"></font></p><p><font face="΢ÈíÑźÚ, sans-serif">Beishan Industrial Zone| Yantian District| Shenzhen 518083</font></p></div></div>
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