<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal">Hi Kapeel,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">If you just want your community annotations to replace models in an existing gene set, we have a tool for this:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><a href="https://github.com/NAL-i5K/GFF3toolkit">https://github.com/NAL-i5K/GFF3toolkit</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">You’d need to run gff3_QC on your annotation files first to make sure your annotations are okay, then use gff3_merge to merge your community annotations with your existing gene set (in gff3 format). If you end up trying this out - we’re
actively developing the GFF3toolkit, so feel free to post an issue if you notice any problems.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hth,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Monica <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">maker-devel <maker-devel-bounces@yandell-lab.org> on behalf of Kapeel Chougule <kapeelc@gmail.com><br>
<b>Date: </b>Friday, June 22, 2018 at 13:53<br>
<b>To: </b>"maker-devel@yandell-lab.org" <maker-devel@yandell-lab.org><br>
<b>Subject: </b>[CAUTION: Suspicious Link][maker-devel] map_forward=1 not mapping reference ID's to output correctly<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<p style="margin-left:.5in"><b>PROCEED WITH CAUTION:</b> This message triggered warnings of
<b>potentially</b> malicious web content. Evaluate this email by considering whether you are expecting the message, along with inspection for suspicious links.
<o:p></o:p></p>
<p style="margin-left:.5in">Questions: Spam.Abuse@wdc.usda.gov<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">Hi,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#2B2C33;letter-spacing:-.15pt;background:#F1F1F4">I am trying to update
<a href="https://de.cyverse.org/dl/d/39D60E88-078D-4CF5-9F3A-D712B714CDD8/community.annotation.gff3">
community annotation</a> in the light of new evidence data but my MAKER runs are not keeping all the genes from the community annotation.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#2B2C33;letter-spacing:-.15pt;background:#F1F1F4"><br>
<br>
</span><o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in;line-height:16.5pt"><span style="font-size:10.5pt;font-family:"Courier New";color:#2B2C33;letter-spacing:-.15pt;background:#F1F1F4">Community annotation feature count: 2 1 bicolor 239969 CDS 266301 exon 51066 five_prime_UTR
34129 gene 47121 mRNA 53708 three_prime_UTR<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in;line-height:16.5pt;background:#F1F1F4">
<span style="font-size:10.5pt;font-family:"Courier New";color:#2B2C33;letter-spacing:-.15pt">MAKER gene count-> <o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in;line-height:16.5pt;background:#F1F1F4">
<span style="font-size:10.5pt;font-family:"Courier New";color:#2B2C33;letter-spacing:-.15pt">awk '$3=="gene"{print}' maker_output.all.gff | grep "Sobic*" | wc -l 21105<o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in;line-height:16.5pt;background:#F1F1F4">
<span style="font-size:10.5pt;font-family:"Courier New";color:#2B2C33;letter-spacing:-.15pt"><o:p> </o:p></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-left:.5in">In the maker_opts.ctl file attached, I did make keep_preds=1 and map_forward=1 which keep all the community gene models even if they dont have evidence support. This was explained here:<br>
<a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data</a><br>
. So not sure why we dont have the all the community gene models mapped in the MAKER output<br>
<br>
Thanks<br>
<br>
Kapeel<br>
-- <o:p></o:p></p>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-family:"Courier New""><o:p> </o:p></span></b></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-family:"Courier New"">Kapeel Chougule<o:p></o:p></span></b></p>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">
<b><span style="font-family:"Courier New"">Computational Scientist Developer II<br>
One Bungtown Road Cold Spring Harbor, NY 11724<br>
<a href="http://www.warelab.org/" target="_blank">http://www.warelab.org/</a></span></b><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<br>
<br>
<br>
This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil
or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
</body>
</html>