[maker-devel] repeats

[Michael Thon]

Hi all - the other issue that we're having with maker is with repeats. We have an annotation of repeats done by a colleague using REPET. I'm passing the annotation in using the rm_gff option and leaving all the other repeat masking options turned off. I found at least one case where a CDS of a final gene model overlaps with a repeat annotation. Does this indicate some problem with my input file or with MAKER?

Thanks
Mike