I have annotated a few plant genome and encounter quite a few cases in which "chimeric" mis-annotations were created. By chimeric I mean two adjacent gene models erroneously fused together by an intron connecting them and creating a single, longer model.
I am wondering if there are any methods / strategies for handling such cases, except for manual curation of course. What do you think would be a more reasonable approach: 1) try to tweak annotation parameters to avoid chimeras, or 2) just accept the fact that chimeras occur and come up with some automatic post-annotation procedure for detection and correction?
I annotated the genomes using MAKER, but I believe this is a general issue that might be relevant for other automatic annotation software as well.
It would be great to hear your suggestions and thoughts about the matter,