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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Could I use “funannotate train and update” with RNA SRA of closely related species (strain)? #888

Open maruiqi0710 opened 1 year ago

maruiqi0710 commented 1 year ago

I want to annotate the genome of a yeast. I do not have RNA data for the genome which I want to annotate, but there are RNA SRA data for other strains of the same species on NCBI. Can I use these data for the train and update steps?

hyphaltip commented 1 year ago

sure can - as long as they are closely related the RNA will align and it can generate genemodels, if the train step fails with these it is usually because the species are too divergent so you will not get sufficient alignments to build at least ~200 training model genes.

Jason Stajich @hyphaltip http://lab.stajich.org

On Tue, Mar 28, 2023 at 7:21 AM maruiqi0710 @.***> wrote:

I do not have RNA data for the genome which I want to annotate, but there are RNA SRA data for other strains of the same species on NCBI. Can I use these data for the train and update steps?

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