[maker-devel] Maker decision of genes when having a long transcript over several proteins

[Qihua Liang]

Dear Maker Dev Team:

I am using Maker for gene annotations and I separate different tracks in the GFF to visualize a genomic region in a genome browser. 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?

I also examine another genomic region where Augustus and SNAP predict a gene; there is no EST hit, but one protein hit. At this case, Maker does not annotate a gene at this region. Is it because a protein hit is not enough for annotating a region and it always requires EST hit?

Thanks
Qihua