[maker-devel] MAKER problem with gff3 file

[Carson Holt]

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, ychliu at genetics.ac.cn 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
> E-mail: ychliu at genetics.ac.cn <mailto:ychliu at genetics.ac.cn>_______________________________________________
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