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Old 12-18-2011, 06:17 PM   #1
Junior Member
Location: Sydney

Join Date: Dec 2011
Posts: 7
Default Genemark-ES and Maker

Hi all,

I've run the MAKER gene annotation pipeline using Genemark for ab-initio gene predictions. However, it seems like Genemark is reporting each gene twice. Does anyone know why this is occurring?

What I have done is trained Genemark using my draft genome. I have then used the .mod file in the MAKER ctrl.exe control file. Is this the correct process?

Here's an example of what I am getting, it's predicting gene 0.0 and gene 0.1, but they are the same thing:

##gff-version 3
scaffold445     .       contig  1       702     .       .       .       ID=scaffold445;Name=scaffold445;
scaffold445     genemark        match           610     621     .       +       .       ID=scaffold445:hit:1234;Name=genemark-scaffold445-abinit-gene-0.0-mRNA-1;_AED=1.00;_eAED=1.00;
scaffold445     genemark        match_part      610     621     .       +       .       ID=scaffold445:hsp:2979;Parent=scaffold445:hit:1234;Name=genemark-scaffold445-abinit-gene-0.0-mRNA-1;Target=genemark-scaffold445-abinit-gene-0.0-mRNA-1 1 12 +;Gap=M12;
scaffold445     genemark        match           610     621     .       +       .       ID=scaffold445:hit:1235;Name=genemark-scaffold445-abinit-gene-0.1-mRNA-1;_AED=1.00;_eAED=1.00;
scaffold445     genemark        match_part      610     621     .       +       .       ID=scaffold445:hsp:2980;Parent=scaffold445:hit:1235;Name=genemark-scaffold445-abinit-gene-0.1-mRNA-1;Target=genemark-scaffold445-abinit-gene-0.1-mRNA-1 1 12 +;Gap=M12;
Sorry if this is an ignorant question, I am quite new to bioinformatics.

Last edited by Rockx; 12-18-2011 at 09:45 PM.
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