est_forward option and low or incorrect orientation transfer
I am using the est_forward=1 #reserve flag for map2assembly option to transfer a transcriptome to the genome and create directly gene models from it. This usually works ok but on a larger genome I only have a transfer rate of 44% from busco
score of cds (gffread extracted). I’m not sure if it’s just transferred 50% as wrong orientation so UTR instead which sometimes happens but not to that scale, or just not transferred because of snps. What settings can I change to test some things out to improve
transfer of transcriptome to genome?