Maker decision of genes when having a long transcript over several proteins
Dear Maker Dev Team:
I am using Maker for gene annotations and I separate different tracks in the GFF to visualize in a genome browser. As in the attached picture, there is a very long Maker gene “maker-chr9-augustus-gene-102.77”. Both Augustus and SNAP predict four short genes at this region. There is one long EST hit and three short protein hit. Maker annotates it as a long gene, I am wondering if it is indicated by EST hit? If annotating three or four short genes is the “correct” way, is it any settings I should change instead of removing the EST evidence?