Training a new organism's genome #336
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KatharinaHoff
DiyaPrabhuram
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AUGUSTUS has been trained for soybean, just not by our group, and I don't
think we were contacted to share the parameter set. You could however get
in touch with the authors of these papers and request parameters. A simple
google search reveals at least two papers from last year.
Otherwise, you can try BRAKER either with RNA-Seq or with protein data for
training AUGUSTUS in a fully automated way. Be sure to softmask the genome
for repeats, beforehand.
…On Mon, Mar 14, 2022 at 2:40 AM DiyaPrabhuram ***@***.***> wrote:
Hi!
I have the genome of soybean (Glycine max). I read through the
command-line docs and it said augustus requires two mandatory parameters to
run - species and queryfile. I have the query file in fasta format but
soybean is not part of the augustus species repertoire. Any suggestions on
what to do in a situation like this? I believe I'm supposed to re-train but
I don't know how to go about doing that.
Thank you in advance!
Cheers,
Diya
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That's super helpful. Thank you! |
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Hi!
I have the genome of soybean (Glycine max). I read through the command-line docs and it said augustus requires two mandatory parameters to run - species and queryfile. I have the query file in fasta format but soybean is not part of the augustus species repertoire. Any suggestions on what to do in a situation like this? I believe I'm supposed to re-train but I don't know how to go about doing that.
Thank you in advance!
Cheers,
Diya
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