maker exons number

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maker exons number

Hu,Ying
Hi, Carson,

I am using MAKER 2.31.6 to annotate a genome. I noticed that exon number in each gene does not start from 1. Can you give me some suggestions how to change the exon number to 1,2,3 .. In each gene? Thansks,

Ying

Here are some examples:

tig00000226|arrow       .       contig  1       43850   .       .       .       ID=tig00000226|arrow;Name=tig00000226|arrow

tig00000226|arrow       maker   gene    26339   27915   .       +       .       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0;Name=augustus_masked-tig00000226|arrow-processed-gene-0.0

tig00000226|arrow       maker   mRNA    26339   27915   .       +       .       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1;Parent=augustus_masked-tig00000226|arrow-processed-gene-0.0;Name=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1;_AED=0.47;_eAED=0.68;_QI=0|0|0|0.75|1|1|4|0|82

tig00000226|arrow       maker   exon    26339   26353   .       +       .       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1:exon:58;Parent=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1

tig00000226|arrow       maker   exon    27490   27636   .       +       .       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1:exon:59;Parent=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1

tig00000226|arrow       maker   exon    27738   27808   .       +       .       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1:exon:60;Parent=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1

tig00000226|arrow       maker   exon    27900   27915   .       +       .       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1:exon:61;Parent=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1

tig00000226|arrow       maker   CDS     26339   26353   .       +       0       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1:cds;Parent=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1

tig00000226|arrow       maker   CDS     27490   27636   .       +       0       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1:cds;Parent=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1

tig00000226|arrow       maker   CDS     27738   27808   .       +       0       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1:cds;Parent=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1

tig00000226|arrow       maker   CDS     27900   27915   .       +       1       ID=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1:cds;Parent=augustus_masked-tig00000226|arrow-processed-gene-0.0-mRNA-1

tig00000226|arrow       maker   gene    5803    6589    .       +       .       ID=maker-tig00000226|arrow-augustus-gene-0.1;Name=maker-tig00000226|arrow-augustus-gene-0.1

tig00000226|arrow       maker   mRNA    5803    6589    .       +       .       ID=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1;Parent=maker-tig00000226|arrow-augustus-gene-0.1;Name=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1;_AED=0.63;_eAED=0.69;_QI=0|0|0|1|0|0|2|0|85

tig00000226|arrow       maker   exon    5803    5975    .       +       .       ID=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1:exon:62;Parent=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1

tig00000226|arrow       maker   exon    6505    6589    .       +       .       ID=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1:exon:63;Parent=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1

tig00000226|arrow       maker   CDS     5803    5975    .       +       0       ID=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1

tig00000226|arrow       maker   CDS     6505    6589    .       +       1       ID=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00000226|arrow-augustus-gene-0.1-mRNA-1


tig00034405|arrow       .       contig  1       104941  .       .       .       ID=tig00034405|arrow;Name=tig00034405|arrow

tig00034405|arrow       maker   gene    40927   51025   .       +       .       ID=maker-tig00034405|arrow-augustus-gene-0.0;Name=maker-tig00034405|arrow-augustus-gene-0.0

tig00034405|arrow       maker   mRNA    40927   51025   .       +       .       ID=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1;Parent=maker-tig00034405|arrow-augustus-gene-0.0;Name=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1;_AED=0.04;_eAED=0.04;_QI=266|1|1|1|0|0|3|0|100

tig00034405|arrow       maker   exon    40927   41273   .       +       .       ID=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1:exon:7157;Parent=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1

tig00034405|arrow       maker   exon    41476   41622   .       +       .       ID=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1:exon:7158;Parent=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1

tig00034405|arrow       maker   exon    50954   51025   .       +       .       ID=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1:exon:7159;Parent=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1

tig00034405|arrow       maker   five_prime_UTR  40927   41192   .       +       .       ID=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1

tig00034405|arrow       maker   CDS     41193   41273   .       +       0       ID=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1

tig00034405|arrow       maker   CDS     41476   41622   .       +       0       ID=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1

tig00034405|arrow       maker   CDS     50954   51025   .       +       0       ID=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.0-mRNA-1

tig00034405|arrow       maker   gene    57931   61565   .       +       .       ID=augustus_masked-tig00034405|arrow-processed-gene-0.2;Name=augustus_masked-tig00034405|arrow-processed-gene-0.2

tig00034405|arrow       maker   mRNA    57931   61565   .       +       .       ID=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1;Parent=augustus_masked-tig00034405|arrow-processed-gene-0.2;Name=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|0.5|0|0.66|1|1|3|0|522

tig00034405|arrow       maker   exon    57931   58962   .       +       .       ID=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1:exon:7160;Parent=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1

tig00034405|arrow       maker   exon    59245   59725   .       +       .       ID=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1:exon:7161;Parent=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1

tig00034405|arrow       maker   exon    61510   61565   .       +       .       ID=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1:exon:7162;Parent=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1

tig00034405|arrow       maker   CDS     57931   58962   .       +       0       ID=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1:cds;Parent=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1

tig00034405|arrow       maker   CDS     59245   59725   .       +       0       ID=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1:cds;Parent=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1

tig00034405|arrow       maker   CDS     61510   61565   .       +       2       ID=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1:cds;Parent=augustus_masked-tig00034405|arrow-processed-gene-0.2-mRNA-1

tig00034405|arrow       maker   gene    90355   94796   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1;Name=maker-tig00034405|arrow-augustus-gene-0.1

tig00034405|arrow       maker   mRNA    90355   94796   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1;Parent=maker-tig00034405|arrow-augustus-gene-0.1;Name=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|0.7|0.72|1|1|1|11|386|425

tig00034405|arrow       maker   exon    90355   90911   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7173;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    91011   91086   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7172;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    91179   91240   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7171;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    91557   91706   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7170;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    92996   93064   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7169;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    93156   93347   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7168;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    93453   93637   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7167;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    93711   93786   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7166;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    93866   93972   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7165;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    94536   94573   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7164;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   exon    94645   94796   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:exon:7163;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     94645   94796   .       -       0       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     94536   94573   .       -       1       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     93866   93972   .       -       2       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     93711   93786   .       -       0       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     93453   93637   .       -       2       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     93156   93347   .       -       0       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     92996   93064   .       -       0       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     91557   91706   .       -       0       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     91179   91240   .       -       0       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     91011   91086   .       -       1       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   CDS     90741   90911   .       -       0       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:cds;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1

tig00034405|arrow       maker   three_prime_UTR 90355   90740   .       -       .       ID=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1:three_prime_utr;Parent=maker-tig00034405|arrow-augustus-gene-0.1-mRNA-1





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