<div dir="ltr"><div><div>Hi Julie,<br><br></div>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 <span class="">v3</span> compared to v2 (300 absent in v2). Some <span class="">genes</span> split in v2 could be rebuilt completely.<br>
• 5b FGS (39,656) => 5b+ (39,475 protein‐coding <span class="">genes</span>)<br>
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RefGen_v3 <span class="">Gene</span> Models include:<br>
• 251 novel <span class="">v3</span> models (new <span class="">gene</span> ids)<br>
• 213 improved models<br>
– 204 one-to‐one updates<br>
– 9 merge two RefGen_v2 models<br>
– 10 received new <span class="">gene</span> ids<br><br></div>A paper describing in more detail the V3 assembly and gene build is near submission. FOr <br><br><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Sep 30, 2014 at 3:45 PM, <a href="mailto:feedback@gramene.org">feedback@gramene.org</a> <span dir="ltr"><<a href="mailto:feedback@gramene.org" target="_blank">feedback@gramene.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">URL : <a href="http://ensembl.gramene.org/Zea_mays/Info/Annotation/" target="_blank">http://ensembl.gramene.org/Zea_mays/Info/Annotation/</a><br>
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Subject : Site Feedback: genome mapping file between B73 RefGen_v2 and B73 RefGen_v3<br>
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Name : Julie Leonard<br>
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Email : <a href="mailto:julie.leonard@syngenta.com">julie.leonard@syngenta.com</a><br>
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Organization: Syngenta<br>
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Comments :<br>
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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>
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Thank you,<br>
Julie<br>
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<a href="http://www.warelab.org/bugs/view.php?id=5042" target="_blank">http://www.warelab.org/bugs/view.php?id=5042</a><br>
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