<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yui_3_16_0_1_1447781830004_3469" dir="ltr"><span id="yui_3_16_0_1_1447781830004_3470">I had to use data from E75 and ucsc.edu. I'm seeing assembly coverage from 2 vectors AC005666.1 and AC011195.14. For fuller span, can look at ENST00000389934, ENST00000582740, ENST00000349033, and ENST00000240361.</span></div> <br><div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"> <font face="Arial" size="2"> On Wednesday, November 11, 2015 5:10 AM, Matthieu Muffato <muffato@ebi.ac.uk> wrote:<br> </font> </div> <br><br> <div class="y_msg_container">Dear Marc,<br clear="none"><br clear="none">Thank you for bringing this to our attention. I have looked in some of <br clear="none">the debug output of the pipeline and I can see that Enredo thinks this <br clear="none">human region is only found syntenic to cat in the 17-way EPO, so the <br clear="none">error goes quite early in the pipeline. I still need to check whether <br clear="none">the anchors were loaded correctly, but the overall coverage stats look <br clear="none">fine. Unfortunately, we don't have all the files for the 8-way EPO. I'll <br clear="none">let you know if I find out what happened to this region<br clear="none"><br clear="none">Matthieu, Ensembl Compara<br clear="none"><div class="yqt8031117661" id="yqtfd60195"><br clear="none">On 04/11/15 12:47, Marc P. Hoeppner wrote:<br clear="none">> Dear EnsEMBL developers,<br clear="none">><br clear="none">> I've noticed that there could be a problem with certain whole genome<br clear="none">> alignments in the current (E82) version of EnsEMBL.<br clear="none">><br clear="none">> Specifically, for the human region 17:58663933-58739040 (and possibly<br clear="none">> others).<br clear="none">><br clear="none">> This region is syntenic on all primate genomes (8 primates EPO) as well<br clear="none">> as 23 amniotes (amniotes Pecan). However, in 17 mammals (EPO), this<br clear="none">> region is only identified as syntenic between human and cat - which I<br clear="none">> suspect is a mistake. I understand that Pecan and EPO use different<br clear="none">> algorithms, but the gene in this region (TEX14) is conserved across all<br clear="none">> mammals (and most vertebrates) and has no obvious homologs that may<br clear="none">> explain off-target alignments.<br clear="none">><br clear="none">> Regards,<br clear="none">><br clear="none">> Marc<br clear="none">><br clear="none"><br clear="none">_______________________________________________<br clear="none">Dev mailing list <a href="mailto:Dev@ensembl.org" shape="rect" ymailto="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br clear="none">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank" shape="rect">http://lists.ensembl.org/mailman/listinfo/dev</a><br clear="none">Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank" shape="rect">http://www.ensembl.info/</a><br clear="none"></div><br><br></div> </div> </div> </div></div></body></html>