<div dir="ltr">Thanks a lot.---Guohong<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, May 20, 2014 at 7:52 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>I've gone ahead and made the change in the devlopment version. It will probably be convenient in most cases, but it's important to note one caveat. Exon features are shared in GFF3 format. So if there are multiple isoforms that contain the same exon, there will only be a single exon line in the GFF3, but it will list several transcript IDs in it's Parent= attribute.</div>
<div><br></div><div>What does that have to do with with the ID= attribute or exon order? Well it means that ID=exon:2 in the first transcript may be the second exon, but in another transcript ID=exon:2 may be the first exon or third exon, etc. This is because there is only a single line for a given exon and it gets shared by all the transcripts. So it will always have the same ID= tag, but will hold a different position in different isoforms (so it's ordinal value will not go along with the ID in those cases). But since most gene calls from MAKER will have only one isoform (default) it could still be convenient in those cases.</div>
<div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span><div class=""><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" target="_blank">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" target="_blank">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><div><div class="h5"><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 <a href="tel:40259%C2%A0%C2%A0%2040666" value="+14025940666" target="_blank">40259 40666</a> . + . ID=maker-scaffold1-snap-gene-0.254-mRNA-1:exon:7;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>
scaffold1 maker exon <a href="tel:40745%C2%A0%C2%A0%2041604" value="+14074541604" target="_blank">40745 41604</a> . + . 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 <a href="tel:40259%C2%A0%C2%A0%2040666" value="+14025940666" target="_blank">40259 40666</a> . + 2 ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>
scaffold1 maker CDS <a href="tel:40745%C2%A0%C2%A0%2041604" value="+14074541604" target="_blank">40745 41604</a> . + 2 ID=maker-scaffold1-snap-gene-0.254-mRNA-1:cds;Parent=maker-scaffold1-snap-gene-0.254-mRNA-1<br>
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