[maker-devel] maker exon number
YING HU
huyingwin at gmail.com
Wed Apr 17 09:23:10 MDT 2019
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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