[maker-devel] Masking is causing problems with exon/CDS boundary predictions

[Salim Bougouffa]

Hi,

I am having trouble with MAKER/AUGUSTUS annotation.

One of the recurrent ones is the example I attach in artemis screenshot. In
red is the gene of interest. There are three GFF files. Top is augustus
standalone that I executed on the non-masked scaffold. The second is maker
annotation and third is the augustus (from maker) on the masked query.


The gene clearly has four exons and three CDS but the masking seem to
somehow cause augustus to get the boundaries wrong for the first and third
CDS and skip the second CDS entirely.

How do I fix this problem?

Best,
/SB
[image: artemis.png]
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