[maker-devel] missing start and stop codons

[Mack, Brian]

I've been looking at the start and stop codons of the maker predicted transcripts after I stripped off the utr with the fasta_tool script and 7% of the transcripts do not have ATG as a start codon. Also 2% do not have TAA, TAG, or TGA as a stop codon. Could these be real start and stop codons and just rare variants, or should I consider these incomplete genes? If I was to turn on the "always_complete" option in Maker what would that actually do?

Thanks,
Brian




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