repetitive sequences in CDS regions

[glopatriello]

Hi everyone!

I am using Augustus(hints-based) to perform an ab initio gene prediction in a non model organism. The obtained results reports some genes with repetitive sequences in CDS region. With manual inspection, I have observed that these repetitive regions were softmasked and according to aligned RNA-seq data these regions should be introns instead. I was wondering how I can increase the Augustus weigths to increase the score for gene models that do not report these repetitive sequences,

Best,
Giulia

[KatharinaHoff]

Fine tuning parameters is a tedious task... and it may even be locus-specific. You could hard mask the sequences that you absolutely don't want to be part of CDS. That might be an easy fix in your case.

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On Fri, Oct 8, 2021 at 10:04 AM glopatriello ***@***.***> wrote: Hi everyone! I am using Augustus(hints-based) to perform an ab initio gene prediction in a non model organism. The obtained results reports some genes with repetitive sequences in CDS region. With manual inspection, I have observed that these repetitive regions were softmasked and according to aligned RNA-seq data these regions should be introns instead. I was wondering how I can increase the Augustus weigths to increase the score for gene models that do not report these repetitive sequences, Best, Giulia — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#319>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJMC6JDLGBKE4URR2LDVGPTUF2QZ5ANCNFSM5FTAVDZA> . 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>.