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genomeannotation / GAG

Generates an NCBI .tbl file of annotations on a genome.
MIT License
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Flag/remove contained genes #190

Closed jannafierst closed 7 years ago

jannafierst commented 7 years ago

I have genes that are contained in others that NCBI is requesting I remove. I see that GAG counts these but I haven't found where the gene names live. Is there a way to get verbose output with these contained genes?

nextgenusfs commented 7 years ago

You should see errors in your tbl2asn discrepancy report about overlapping genes. Its difficult to determine automatically which gene should be removed if two overlap? Often times it is a tRNA prediction inside an intron, if that is the case I typically just remove the tRNA model.

jannafierst commented 7 years ago

Okay, thanks!