<div dir="ltr">Hi Daniel, I am using maker-2.31.5.---Guohong<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, May 20, 2014 at 3:34 PM, Daniel Ence <span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Guohong,<br>
<br>
What version of MAKER are you running?<br>
<br>
Thanks,<br>
Daniel<br>
<br>
<br>
On May 19, 2014, at 9:43 PM, Guohong Cai <<a href="mailto:caigh02@gmail.com">caigh02@gmail.com</a>><br>
<div><div class="h5"> wrote:<br>
<br>
> Hi Carson,<br>
><br>
> 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>
> Guohong<br>
><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>
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</blockquote></div><br></div>