Dear all,
Today I used Tophat to map the reads from RNA-Seq, and had a look at the results using "visaulization" function. In some regions I can see splice junctions calculated by Tophat, but I don't see any reads mapping to this region. Is this a bit strange? I thought "splice junction" is calculated from the mapped reads.
However, I think cufflinks only uses "accepted hits" as input, maybe it is not a big problem that "splice junction' is not accurate.
Am I right? Was there something wrong when I mapped my reads with tophat?
Hope you can help me figure it out.
Looking forward to hearing from you.
Jiwen