Hi everyone, I am in the process of predicting genes from a non-model organism using the gene predicting software MAKER. I performed a first run of prediction using default parameters and noticed that some of the predicted genes are partially predicted (ie missing either the start or stop codon). I would like to predict only complete genes (ie genes with both start and stop codons).
My question is, what part of the .ctl files should I edit so as to tell MAKER to only predict complete genes. I came across the option below in the maker_opts.ctl file:
always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 = no
If I change the value from 0 to 1, would it force the partially predicted genes to have the start and stop codons even if its wrong, introducing errors? Thanks in advance