<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Hiram<div><br></div><div>I don’t believe this is on our website. Specifically the data in the chain files for the mapping you’re highlighting are from the assembly tables in the core schema. The best description of this is in:</div><div><br></div><div><a href="https://github.com/Ensembl/ensembl/blob/release/110/misc-scripts/assembly/README">https://github.com/Ensembl/ensembl/blob/release/110/misc-scripts/assembly/README</a><br></div><div><br></div><div>The quick description is to look for indexical clone usage and then backfill the remaining bits using blastz. The 37 to 38 mapping were performed using this method if I remember correctly. </div><div><br></div><div>Andy</div><div><br><div>
<meta charset="UTF-8"><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); 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; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="text-align: start; text-indent: 0px; overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;">------------<br></div><div>I sometimes send emails out of hours; I do not expect a response outside of your working hours.</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;"><br></div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;">Andrew Yates - Genomics Technology Infrastructure Team Leader, Joint-PI Ensembl Project</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;">The European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Genome Campus<br>Hinxton, Cambridge<br>CB10 1SD, United Kingdom<br>Tel: +44-(0)1223-492538<br>Fax: +44-(0)1223-494468<br>Skype: andy.yates.ebi<br>https://www.ebi.ac.uk/<br>https://www.ensembl.org/</div></div></div></div></div></div></div></div></div></div></div></div>
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<div><br><blockquote type="cite"><div>On 27 Sep 2023, at 23:45, Hiram Clawson <hiram@soe.ucsc.edu> wrote:</div><br class="Apple-interchange-newline"><div><div>Good Afternoon Ensembl:<br><br>Can you supply a pointer to the documentation that describes the procedures<br>used to make the 'assembly mapping' chain file available at:<br><br> http://ftp.ensembl.org/pub/assembly_mapping/homo_sapiens/GRCh37_to_GRCh38.chain.gz<br><br>It must be close to this page somewhere:<br><br> http://useast.ensembl.org/info/genome/compara/analyses.html<br><br>I'm looking for more detail than just 'lastz output is chained'<br><br>I know it must be somewhere on the Ensembl web site, but I'm not immediately<br>finding that. Thank you for your assistance.<br><br>--Hiram<br><br><br><br>_______________________________________________<br>Dev mailing list Dev@ensembl.org<br>Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org<br>Ensembl Blog: http://www.ensembl.info/<br></div></div></blockquote></div><br></div></body></html>