<html xmlns:v="urn:schemas-microsoft-com:vml" 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:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@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:12.0pt;
font-family:"Times New Roman",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;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.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><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thank you. Worked perfectly.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Craig<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Carson Holt [mailto:carsonhh@gmail.com]
<br>
<b>Sent:</b> Monday, May 11, 2015 11:41 AM<br>
<b>To:</b> Craig Coleman<br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] creating fasta ids<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Pass in GeneMark results as pred_gff if you were using model_gff. By using model_gff you are essentially telling MAKER to protect certain information in the Name tags as well as to keep all models regardless of evidence support from that
file.<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Because of the way you ran things, when you currently move to the maker_map_ids step it builds new names off of the ID= portion because Name= has a specific protected meaning in GFF3 format, so if your Name= and ID= tags are not identical
then the script knows they are user supplied values and cannot assume they are alterable.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">—Carson<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On May 8, 2015, at 3:54 PM, Craig Coleman <<a href="mailto:craig_coleman@byu.edu">craig_coleman@byu.edu</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Hi,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I have a fungal genome that I successfully ran through Maker. Rather than running GeneMark directly in Maker I ran it separately and generated a gff file. I provided this
gff file to Maker and ran SNAP and Augustus as well. The GeneMark gff3 file contained unique IDs for genes that are carried over into the protein and transcript fasta files. These IDs are included in the Maker gff file as the name given for the mRNA feature
but Maker creates a different ID for the GeneMark generated features in the gff file. When I run maker_map_ids to create a mapping file of gene and transcript IDs, the program uses the Maker generated ID instead of the GeneMark generated name. Then when
I run map_fasta_ids the Maker IDs in the map file do not match the names of the GeneMark proteins and transcripts in the fasta file. Protein and transcript models generated by SNAP and Augustus map just fine. I am hoping someone has a suggestion on how to
solve this problem.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Craig Coleman<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
maker-devel mailing list<br>
</span><a href="mailto:maker-devel@box290.bluehost.com"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">maker-devel@box290.bluehost.com</span></a><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><br>
</span><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#954F72">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</span></a><o:p></o:p></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</body>
</html>