Re: [maker-devel] maker-devel post from brian.mack@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.

From: "Mack, Brian - ARS" <brian...@usda.gov>

Subject: genemark-es training on masked genome

Date: May 17, 2021 at 9:47:57 AM MDT

To: "maker...@yandell-lab.org" <maker...@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-dev...@yandell-lab.org

Subject: confirm 9305bcd5964821ff5fff547bdb1b0466c9c50b58

Date: May 17, 2021 at 9:48:09 AM MDT

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