<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>I can do that. Just a note of caution though. The ID= attribute is not protected (it's just an identifier to relate things to one another for correct parentage). Downstream scripts that use or manipulate GFF3 files can change it (so relying on it to always be the same or even be informative is not guaranteed).</div><div><br></div><div>--Carson</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> Guohong Cai <<a href="mailto:caigh02@gmail.com">caigh02@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, May 19, 2014 at 9:43 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] Maker exon number<br></div><div><br></div><div dir="ltr"><div><div>Hi Carson,<br><br></div>I am using MAKER to annotate a few small genomes. When looking through the gff file, I notice that the exon numbers do not start from 0 or 1 for each gene. Only the first gene in a scaffold start with exon 0. If the first gene has 3 exons (0-2), then the second gene will start from exon 3 (an example is shown below). It seems many people would prefer that in each gene, the first exon be exon 1. Is it possible to make such a change? Thanks.<br><br></div>Guohong<br><div><br><br>scaffold1 . contig 1 347483 . . . ID=scaffold1;Name=scaffold1<br>scaffold1 maker gene 106 2985 . + . ID=genemark-scaffold1-processed-gene-0.0;Name=genemark-scaffold1-processed-gene-0.0<br>
scaffold1 maker mRNA 106 2985 . + . ID=genemark-scaffold1-processed-gene-0.0-mRNA-1;Parent=genemark-scaffold1-processed-gene-0.0;Name=genemark-scaffold1-processed-gene-0.0-mRNA-1;_AED=0.12;_eAED=0.13;_QI=0|0|0|1|1|1|3|0|840<br>
scaffold1 maker exon 106 1684 . + . ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:exon:0;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1<br>scaffold1 maker exon 1878 2440 . + . ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:exon:1;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1<br>
scaffold1 maker exon 2605 2985 . + . ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:exon:2;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1<br>scaffold1 maker CDS 106 1684 . + 0 ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:cds;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1<br>
scaffold1 maker CDS 1878 2440 . + 2 ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:cds;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1<br>scaffold1 maker CDS 2605 2985 . + 0 ID=genemark-scaffold1-processed-gene-0.0-mRNA-1:cds;Parent=genemark-scaffold1-processed-gene-0.0-mRNA-1<br>
scaffold1 maker gene 38466 41604 . + . ID=maker-scaffold1-snap-gene-0.254;Name=maker-scaffold1-snap-gene-0.254<br>scaffold1 maker mRNA 38466 41604 . + . ID=maker-scaffold1-snap-gene-0.254-mRNA-1;Parent=maker-scaffold1-snap-gene-0.254;Name=maker-scaffold1-snap-gene-0.254-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|0.83|1|1|6|0|892<br>
scaffold1 maker exon 38466 38511 . + . ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:3;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>scaffold1 maker exon 38616 38742 . + . ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:4;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>
scaffold1 maker exon 38831 39986 . + . ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:5;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>scaffold1 maker exon 40073 40154 . + . ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:6;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>
scaffold1 maker exon 40259 40666 . + . ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:7;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>scaffold1 maker exon 40745 41604 . + . ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:8;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>
scaffold1 maker CDS 38466 38511 . + 0 ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>scaffold1 maker CDS 38616 38742 . + 2 ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>
scaffold1 maker CDS 38831 39986 . + 1 ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>scaffold1 maker CDS 40073 40154 . + 0 ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>
scaffold1 maker CDS 40259 40666 . + 2 ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>scaffold1 maker CDS 40745 41604 . + 2 ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br><br></div></div>
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