How to handle mis-annotated chimeric genes?
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7 months ago
liorglic ▴ 460

Hello,
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,

Cheers.

chimeric MAKER curation annotation • 142 views
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