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Gaius-Augustus / Augustus

Genome annotation with AUGUSTUS
http://bioinf.uni-greifswald.de/webaugustus/
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Masking #295

Open Nickolaz47 opened 3 years ago

Nickolaz47 commented 3 years ago

I would like to know how AUGUSTUS treats masked regions on genome. I have a softmasked genome and I did a prediction on it, but I do not know if AUGUSTUS ignores these regions or predicts on them. If it predicts, how could I recover only genes predicted outside masked regions ?

MarioStanke commented 3 years ago

In newer versions by default and in any case when --softmasking=1 is specified, AUGUSTUS treats each masked region as a little more likely to be not in an exon. Predicted exons can overlap masked regions but it is increasingly discouraged with the length of the overlap. How could I recover only genes predicted outside masked regions ? That is not identified by augustus and up to you, as you also have to define what that is supposed to mean. You want to ignore a long gene only because a single base was masked?