MAKER problem with gff3 file

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MAKER problem with gff3 file

ychliu@genetics.ac.cn
Dear MAKER developers,
        I recently use the MAKER to do gene annotation. But even I use the gff3 file as the EST evidence, the result shows no gene that marked by est2genome (I do use the parameter est2genome=1). It may means that the gff3 seems doesn't work. So what's the problem? How can I solve it? Eager for you assistance.
        Faithfully yours.
        Yucheng Liu


Yucheng Liu
Institute of Genetics and Developmental Biology, CAS
Beijing, 100101 China
Tel: 86-010-64801362

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Re: MAKER problem with gff3 file

Carson Holt-2
The est2genome=1 one option in MAKER2 only works with input fasta files because it’s based on Exonerate’s est2genome alignments. It does not with with GFF3 input (gff3 is missing some things that are in the exonerate report). MAKER3 however will let you do this with GFF3 input (it goes back and tries to predict missing info that Exonerate would have produced).

—Carson


On Apr 2, 2019, at 7:21 PM, [hidden email] wrote:

Dear MAKER developers,
        I recently use the MAKER to do gene annotation. But even I use the gff3 file as the EST evidence, the result shows no gene that marked by est2genome (I do use the parameter est2genome=1). It may means that the gff3 seems doesn't work. So what's the problem? How can I solve it? Eager for you assistance.
        Faithfully yours.
        Yucheng Liu


Yucheng Liu
Institute of Genetics and Developmental Biology, CAS
Beijing, 100101 China
Tel: 86-010-64801362
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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