<div dir="ltr"><div><div>Sorry, message went unfinished... <br></div>Last just wanted to point out the assembly converter tool at <a href="http://ensembl.gramene.org/tools.html">http://ensembl.gramene.org/tools.html</a> which will allow you to convert coordinates between the v2 and v3 assemblies.<br></div><div>Hope this helps!<br></div><div><br></div>Marcela<br><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Sep 30, 2014 at 6:17 PM, Monaco, Marcela <span dir="ltr"><<a href="mailto:mmonaco@cshl.edu" target="_blank">mmonaco@cshl.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">Hi Julie,<br>
<br>
Unfortunately we do not have a file like the one with discontinued IDs generated for the 5a gene set. If it helps, these are the differences between the v2 and v3 (filtered/coding) gene sets:<br>
<br>
• Over 2,100 FLcDNAs had longer alignments to v3 compared to v2 (300 absent in v2). Some genes split in v2 could be rebuilt completely.<br>
• 5b FGS (39,656) => 5b+ (39,475 protein‐coding genes)<br>
<br>
RefGen_v3 Gene Models include:<br>
• 251 novel v3 models (new gene ids)<br>
• 213 improved models<br>
– 204 one-to‐one updates<br>
– 9 merge two RefGen_v2 models<br>
– 10 received new gene ids<br>
<br>
A paper describing in more detail the V3 assembly and gene build is near submission. FOr<br>
<br>
<br>
</span><span class="">On Tue, Sep 30, 2014 at 3:45 PM, <a href="mailto:feedback@gramene.org">feedback@gramene.org</a><mailto:<a href="mailto:feedback@gramene.org">feedback@gramene.org</a>> <<a href="mailto:feedback@gramene.org">feedback@gramene.org</a><mailto:<a href="mailto:feedback@gramene.org">feedback@gramene.org</a>>> wrote:<br>
URL : <a href="http://ensembl.gramene.org/Zea_mays/Info/Annotation/" target="_blank">http://ensembl.gramene.org/Zea_mays/Info/Annotation/</a><br>
<br>
Subject : Site Feedback: genome mapping file between B73 RefGen_v2 and B73 RefGen_v3<br>
<br>
Name : Julie Leonard<br>
<br>
</span>Email : <a href="mailto:julie.leonard@syngenta.com">julie.leonard@syngenta.com</a><mailto:<a href="mailto:julie.leonard@syngenta.com">julie.leonard@syngenta.com</a>><br>
<span class=""><br>
Organization: Syngenta<br>
<br>
Comments :<br>
<br>
Hi. I wanted to know if you have created a gene and/or transcript mapping file between B73 RefGen_v2 (5b.60) and B73 RefGen_v3 (AGPv3). If so, is this available for the public. I'm looking for something similar to this file: <a href="ftp://ftp.gramene.org/pub/gramene/maizesequence.org/release-5a/working-set/4a_discontinued_ids.txt" target="_blank">ftp://ftp.gramene.org/pub/gramene/maizesequence.org/release-5a/working-set/4a_discontinued_ids.txt</a>.<br>
<br>
Thank you,<br>
Julie<br>
<br>
<a href="http://www.warelab.org/bugs/view.php?id=5042" target="_blank">http://www.warelab.org/bugs/view.php?id=5042</a><br>
<br>
<br>
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