I'm currently using tophat 2.04 with --fusion-search to discover fusion transcripts in a non-well annotated genome. I created my own annotation with the gene sequences of a related species (which is annotated). So I have the genome fasta file and a gff for the annotation. I ran tophat 2.0.4 on all my samples and I now want to execute tophat-fusion-post. I read tophat's manual ( here ) but I have difficulties understanding how to execute tophat-fusion-post on non-human samples. What about refGene.txt and ensGene.txt? Do I have to create them starting from the annotation? Same question for the blast databases.
Thanks a lot for your help,