Masking

[Nickolaz47]

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]

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?