Automatically annotate gene loci

Question

[rtrende]

My lab has recently received a new strain of mice with a large (hundreds of kb) transgene containing many genes from another common species. The collaborator that we received the mice from sent us the sequence of the transgene, but none of the genes were annotated. Is there a tool to help us automatically annotate the genes in the transgene? More specifically, we are planning to do single-cell RNA sequencing, so we need a tool that will produce a .gtf file that we can use as a reference for that