I am trying to get fusions of Endogenous Retroviral elements (ERVs) and genes/lncRNA. There are some nice tools out there work quite nicely for gene-gene fusions e.g. fusioncatcher etc.
I am searching something which could work well for ERVs and genes,
I already did something by my own, manipulating outputs from some tools, but there was quite low overlap and moreover results were inconsistent among replicates.
I would appreciate if you can please advice me anything on this.
PS: If I can analyze outputs from TopHat2-fusion or STAR outputs in someway where I get more and significant fusions.