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Rockx 12-18-2011 07:17 PM

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:

Code:

##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.


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