I am using bioconductor package "chimera" for fusion detection and am encountering weird error. Basically the annotation for one of the fusion partner genes is wrong even though it is mapping to correct genomic co-ordinate. If you look at the following GRanges object:

GRanges object with 1 range and 5 metadata columns:

      seqnames                 ranges strand | KnownGene KnownTranscript

  [1]     chr6 [117650610, 117650640]      - |      GOPC            <NA>

      KnownExonNumber KnownTranscriptStrand FusionJunctionSequence

It is mapping to GOPC instead of ROS1. I am wondering if the annotation file being used in chimera is "UCSC hg19" or not? I appreciate any help.

Thanks,

Sri