[maker-devel] maker-devel post from brian.mack at usda.gov requires approval

[Carson Holt]

No requirement to train on a masked genome.  If I’m not mistaken GeneMark splits up the genome on long stretches of N, so it may make training faster, but it may also split contains on some introns.

—Carson


> to approve or deny the request.
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> From: "Mack, Brian - ARS" <brian.mack at usda.gov <mailto:brian.mack at usda.gov>>
> Subject: genemark-es training on masked genome
> Date: May 17, 2021 at 9:47:57 AM MDT
> To: "maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> 
> 
> Hi,
>  
> I’m using MAKER for a fungal genome and I was wondering if it is recommended to train genemark-es on a masked genome? If so, would running just the repeat masking step with MAKER and using the masked files from the “Void” directories be appropriate (cat *output/*datastore/*/*/*/*Void*/query.masked.fasta > masked_genome.fasta) ?
>  
> Thanks,
> Brian
> 
> 
> 
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> From: maker-devel-request at yandell-lab.org <mailto:maker-devel-request at yandell-lab.org>
> Subject: confirm 9305bcd5964821ff5fff547bdb1b0466c9c50b58
> Date: May 17, 2021 at 9:48:09 AM MDT
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