Training a new organism's genome

[DiyaPrabhuram]

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

[KatharinaHoff]

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.

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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 — Reply to this email directly, view it on GitHub <#336>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJMC6JCDB3SSYXTUL6S4YHTU72KKDANCNFSM5QUFDRDA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[DiyaPrabhuram]

That's super helpful. Thank you!