I've been testing Apollo for use in collaborative manual annotation of herpesvirus genomes. It seems to be working well enough so far, but there are some inconveniences that slow down the workflow quite a bit. I haven't been able to figure out how to change these behaviors, but I'm hoping maybe I missed something in the documentation. Specifically:
1. Whenever I drag a gene model from a GFF3 track to the "User-created" canvas, it automatically adjusts the coding region to the longest detected ORF. Many herpesviral genes occur in co-terminal clusters with long 3'UTRs for the upstream genes, so this behavior is often not desirable. It is possible to manually fix the translation start each time, but I'm hoping there is a user-level or server-level config that can be set to disable this behavior.
2. Apollo seems to group overlapping transcripts into genes by default when dragged into the annotation canvas. For similar reasons as above (frequent clusters of co-terminal transcripts coding for different proteins and with different TSS/promoters), this is again inconvenient for herpesvirus genomes. It's not too difficult to use "Dissociate Transcript from Gene" each time, but then all of the functional annotations from the original gene that was dragged are lost and have to be re-entered manually. Is there a way to disable this behavior?