[maker-devel] Query on genemark results

[Carson Holt]

The previous bug was a complete lack of GeneMark results in the GFF3, not
just a lack of consensus models from GeneMark.  It is possible to get no
consensus models from GeneMark if they score poorly.  Send me the GFF3
results of your larger contigs and I can review it and tell you if any
models are being improperly categorized.

Thanks,
Carson


On 12-10-28 1:50 PM, "kokwei" <kokwei86 at gmail.com> wrote:

>Hi,
>
>I have the same problems as posted by André Gomes on 10/4/10. I still
>have the same problems even though using the current available version
>of maker (maker 2.1 and maker 2.26 beta version).
>
>I have tried to do the gene prediction on eukaryotic genome using 3
>ab-initio gene predictors (SNAP,  Augustus and GeneMark-ES) using Maker.
>From the fasta_merge output, I have 3 separate files of gene models
>($prefix.all.maker.augustus_masked.proteins.fasta,
>$prefix.all.maker.snap_masked.proteins.fasta and
>$prefix.all.maker.genemark.proteins.fasta) and one
>$prefix.all.maker.proteins.fasta (I presume this should be the consensus
>gene models from 3 predictors' results, right?).
>
> From the consensus gene models file, I don't see even one result from
>genemark but all from snap/augustus only. Is that normal?
>Also from the file naming and gene model label in final gff file, it's
>showing that genemark is not masked like those of augustus and snap? Is
>that true? Why only augustus and snap masked but not genemark? Please
>assist and thanks for your helps.
>
>Kok Wei
>
>
>
>
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