I am currently working on RNA sequencing data from my model organism Volvox carteri for the first time. After checking the mapping in IGV i found that several reads map to regions in the genome, where no gene prediction is located. How can I enhance complete the list of currently annotated genes (that are currently in a GFF3 file) with newly predicted ones based on the RNA-Seq mappings? Is there a tool for this?
In the process i would like to keep the old genes with the old names and just add the new ones.