<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>There has been some post processing of the GFF3. It is not an original MAKER result file. I can tell based on the ID's (maker doesn't assign numerical IDs).</div><div><br></div><div>Most likely it was processed to make exons unique without having dual parentage. Normally if the same exon is found in two transcripts it will have two parents separated by a comma. I imaging that the post processing script duplicated the exon, creating independent IDs and split the parents, but left the Name= tag the same. Since the Name= tag was based off of the first transcript the exon belonged to, it stayed the same.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Kang, Yang Jae" <<a href="mailto:kangyangjae@gmail.com">kangyangjae@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Sunday, 12 May, 2013 11:53 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] exon numbering bug?<br></div><div><br></div><div 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"><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"><meta name="Generator" content="Microsoft Word 14 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div lang="KO" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal"><span lang="EN-US">Hello<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p><p class="MsoNormal"><span lang="EN-US">I want to check this is bug or my misunderstanding. The following is the gff3 result of maker pipeline. <o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">I think those red marks should be mRNA-2. This type of error was found only at exon<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker mRNA 604856 612126 . + . ID=211342;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2;Parent=211320<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="color:red">scaffold_22 maker exon 604856 605185 0.51 + . ID=211343;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2788;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="color:red">scaffold_22 maker exon 608362 608456 0.51 + . ID=211344;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2791;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="color:red">scaffold_22 maker exon 610193 610286 0.51 + . ID=211345;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2792;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="color:red">scaffold_22 maker exon 610583 610714 0.51 + . ID=211346;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2793;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="color:red">scaffold_22 maker exon 610838 610942 0.51 + . ID=211347;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2794;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US" style="color:red">scaffold_22 maker exon 611458 612126 0.51 + . ID=211348;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-1:exon:2795;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker five_prime_UTR 604856 604972 . + . ID=211349;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:UTR1;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker CDS 604973 605185 . + 0 ID=211350;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2905;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker CDS 608362 608456 . + 0 ID=211351;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2906;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker CDS 610193 610286 . + 1 ID=211352;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2907;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker CDS 610583 610714 . + 0 ID=211353;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2908;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker CDS 610838 610942 . + 0 ID=211354;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2909;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker CDS 611458 611661 . + 0 ID=211355;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:cds:2910;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker three_prime_UTR 611662 612126 . + . ID=211356;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:UTR2;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker start_codon 604973 604975 . + . ID=211357;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:start1;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US">scaffold_22 maker stop_codon 611659 611661 . + . ID=211358;Name=maker-scaffold_22-augustus-gene-0.532-mRNA-2:stop2;Parent=211342<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p><p class="MsoNormal"><span lang="EN-US">Thank you!<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p><p class="MsoNormal" align="left" style="text-align:left"><b><span lang="EN-US">Kang, Yang Jae <o:p></o:p></span></b></p><p class="MsoNormal" align="left" style="text-align:left"><span lang="EN-US">Ph.D.<o:p></o:p></span></p><p class="MsoNormal" align="left" style="text-align:left"><span lang="EN-US">Cropgenomics Lab.<o:p></o:p></span></p><p class="MsoNormal" align="left" style="text-align:left"><span lang="EN-US">College of Agriculture and Life Science<o:p></o:p></span></p><p class="MsoNormal" align="left" style="text-align:left"><span lang="EN-US">Seoul National University <o:p></o:p></span></p><p class="MsoNormal" align="left" style="text-align:left"><span lang="EN-US">Korea<o:p></o:p></span></p><p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p></div></div></div>_______________________________________________
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