I have used STAR aligner followed by Chimera package for further filtering with the aim to detect fusion genes. Now the issue is that I have used hg19 genome reference and Gencode v19 for annotation in STAR. But, perhaps the annotation used in Chimera (possibly UCSC known gene) is not the same. Can anyone suggest me how to modify the annotation used in Chimera tool? Can I use Gencode annotation in Chimera package?