This seems like an obvious question, but I couldn't find an obvious answer anywhere.
Tophat-fusion-post output includes the orientation of each fusion partner. I'm noticing that a really high percentage (close to 50%) of my reported fusion events have 1 or both partners with orientations opposite to the way they read in the genome, e.g.:
Genome:
Gene 1 ------> Gene 2 ------>
Fusion:
Gene 1 ------> <------Gene 2
Unless I'm missing something, it seems like these would very rarely produce a functional, chimeric transcript? Is there a reason Tophat-fusion-post doesn't filter these during the Blast search?
This is with Illumina HiSeq PE reads by the way.
Tophat-fusion-post output includes the orientation of each fusion partner. I'm noticing that a really high percentage (close to 50%) of my reported fusion events have 1 or both partners with orientations opposite to the way they read in the genome, e.g.:
Genome:
Gene 1 ------> Gene 2 ------>
Fusion:
Gene 1 ------> <------Gene 2
Unless I'm missing something, it seems like these would very rarely produce a functional, chimeric transcript? Is there a reason Tophat-fusion-post doesn't filter these during the Blast search?
This is with Illumina HiSeq PE reads by the way.